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URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo
When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page
coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics
coverage: Mass spectrometer output files and spectra interpretation
creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>
creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de>
creator: David Cox <david.cox <-at-> sciex.com>
creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se>
creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
creator: Jeroen Van Goey <j.vangoey <-at-> instadeep.com>
creator: Jonathan Hunter <jhunter <-at-> ebi.ac.uk>
creator: Joshua Klein <jaklein <-at-> bu.edu>
creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de>
creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
creator: Mathias Walzer <walzer <-at-> ebi.ac.uk>
creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de>
creator: Nithu Sara John <nithu <-at-> ebi.ac.uk>
creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch>
creator: Samuel Wein <sam <-at-> openms.de>
creator: Wout Bittremieux <wout.bittremieux <-at-> uantwerpen.be>
creator: Yasset Perez-Riverol <yperez <-at-> ebi.ac.uk>
publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group
The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format.
'Entity A' has value type 'Entity B', such as xsd:float.
Proteomics Standards Initiative Mass Spectrometry Vocabularies.
A reference number relevant to the sample under study.
A reference string relevant to the sample under study.
The chemical phase of a pure sample, or the state of a mixed sample.
Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
The method by which gas phase ions are generated from the sample.
OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer.
This term was made obsolete because it was replaced by scan polarity (MS:1000465).
OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted.
This former purgatory term was made obsolete.
Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
Which of the available standard measures is used to define whether two peaks are separate.
OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z.
Accuracy is the degree of conformity of a measured mass to its actual value.
The time that an analyzer started a scan, relative to the start of the MS run.
OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum.
OBSOLETE This former purgatory term was made obsolete.
Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low).
Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used.
Describes the acquisition data type produced by a tandem mass spectrometry experiment.
Status of the reflectron, turned on or off.
The length of the field free drift space in a time of flight mass spectrometer.
OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion.
Final MS level achieved when performing PFF with the ion trap (e.g. MS E10).
A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity.
Type of detector used in the mass spectrometer.
Method by which detector signal is acquired by the data system.
The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height.
The rate of signal sampling (measurement) with respect to time.
This term was made obsolete because it was replaced by instrument model (MS:1000031).
Instrument model name not including the vendor's name.
Free text description of a single customization made to the instrument; for several modifications, use several entries.
The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution.
The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions.
Spectral peak processing conducted on the acquired data to convert profile data to centroided data.
OBSOLETE Terms to describe the polarity setting of the instrument.
This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186).
This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031).
This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010).
Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
Number of net charges, positive or negative, on an ion.
Intensity of ions as measured by the height or area of a peak in a mass spectrum.
Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.
Fragmentation method used for dissociation or fragmentation.
Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
OBSOLETE Energy units are represented in either eV or Joules.
This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111).
State if the sample is in emulsion form.
State if the sample is in solution form.
State if the sample is in suspension form.
OBSOLETE Chromatographic conditions used to obtain the sample.
Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
The sample is directly inserted into the ion source, usually on the end of a heatable probe.
Inlet used for introducing the liquid sample into an electrospray ionization source.
A sample introduction method in which a discrete sample aliquot is injected into a continuous carrier solvent stream and transported to the ionization source without separation, producing a transient analytical signal.
A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction.
A sample introduction method in which a sample solution is continuously delivered to the ionization source at a constant flow rate without separation.
A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity.
A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane.
Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules.
Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules.
A division of flowing stream of liquid into two streams.
Method for generating ions from a solution of an analyte.
A sample inlet method involving a reservoir.
A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber.
A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample.
Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
atmospheric pressure chemical ionization
The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization.
OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
This term was made obsolete because it was replaced by electron ionization (MS:1000389).
A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended.
The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization.
The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
matrix-assisted laser desorption ionization
Polarities of the scans of a run are all negative.
Polarities of the scans of a run are all positive.
A linear ion trap mass analyzer where ions are ejected along the axis of the analyzer.
A device based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
fourier transform ion cyclotron resonance
A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z.
A device that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
A linear ion trap mass analyzer where ions are ejected along the radius of the analyzer.
Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
An attribute of resolution when recording the detector response in absence of the analyte.
A measure of resolution represented as width of the peak at half peak height.
An attribute of resolution when the ratio between adjacent signals is 10% of the signal height.
OBSOLETE When resolution is constant with respect to m/z.
This child of the former purgatory term resolution type was made obsolete.
OBSOLETE When resolution is proportional with respect to m/z.
OBSOLETE A variation of instrument where a selected mass is scanned.
This child of the former purgatory term Scan Function was made obsolete.
OBSOLETE Please see Single Ion Monitoring.
High to low direction in terms of m/z of the scan for scanning analyzers.
Low to high direction in terms of m/z of the scan for scanning analyzers.
The mass scan is done in exponential mode.
OBSOLETE The mass scan is done in linear mode.
This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199).
The mass scan is done in quadratic mode.
OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring.
OBSOLETE This term is not recommended. See Selected Reaction Monitoring.
This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206).
OBSOLETE The specific scan function or process that will record a precursor ion spectrum.
OBSOLETE The specific scan function or process that records product ion spectrum.
OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum.
This term was made obsolete because it was replaced by single ion monitoring (MS:100205).
This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206).
A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse.
A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected.
A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier.
Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector.
A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons.
A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device.
An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate.
A detector system commonly used in inductively coupled plasma mass spectrometers.
A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected.
Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers.
A device for converting a signal of sporadic pluses into a digital representation of their time indices.
A detector acquisition mode used for detecting transient signals.
ThermoFinnigan from Thermo Electron Corporation instrument model.
Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
The number of counted events observed in one or a group of elements of a detector.
The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity.
The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra.
Fragmentation that results from the collision of an ion with a surface.
OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J.
This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).
Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
Applied Biosystems/MDS SCIEX Q 4000 TRAP MS.
Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS.
Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
Applied Biosystems/MDS SCIEX API 150EX MS.
Applied Biosystems/MDS SCIEX API 150EX Prep MS.
Applied Biosystems/MDS SCIEX API 2000 MS.
Applied Biosystems/MDS SCIEX API 3000 MS.
Applied Biosystems/MDS SCIEX API 4000 MS.
Bruker Daltonics' autoflex II: MALDI TOF.
Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF.
Waters magnetic sector based AutoSpec Ultima NT MS.
Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI.
Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI.
Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI.
Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS.
Waters (triple) quadrupole based Ultima.
Applied Biosystems/MDS SCIEX SymBiot I MS.
Applied Biosystems/MDS SCIEX SymBiot XVI MS.
Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF.
Applied Biosystems/MDS SCIEX Voyager-DE PRO MS.
Applied Biosystems/MDS SCIEX Voyager-DE STR MS.
The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space.
OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition.
This child of the former purgatory term ion attribute was made obsolete.
OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance.
OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended.
The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state.
OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg.
This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).
OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy.
OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization.
OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom.
A section of a mass spectrometer in which there are no electric or magnetic fields.
OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule.
This child of the former purgatory term ion reaction was made obsolete.
OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used.
This term was made obsolete because it was replaced by ionization efficiency (MS:1000392).
OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion.
OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
This child of the former purgatory term mass spectrometry was made obsolete.
The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer.
OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom.
OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion.
Mass of a molecule measured in unified atomic mass units (u or Da).
OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.
OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
This child of the former purgatory term mass spectrometer was made obsolete.
Photoionization of an atom or molecule in which in two or more photons are absorbed.
OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms.
OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value.
OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions.
A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably.
OBSOLETE The height or area of a peak in a mass spectrum.
This term was made obsolete because it was replaced by base peak intensity (MS:1000505).
OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states.
OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported.
This term was made obsolete because it was replaced by mass resolving power (MS:1000800).
Representation of the total ion current detected in each of a series of mass spectra versus time.
The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region.
OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg.
This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221).
OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy.
Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer.
atmospheric pressure matrix-assisted laser desorption ionization
Any ionization process in which ions are formed in the gas phase at atmospheric pressure.
OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382).
A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation.
blackbody infrared radiative dissociation
OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer.
The formation of ions from a solid or liquid material after the rapid vaporization of that sample.
A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
A legacy liquid chromatography-mass spectrometry interface in which a minor fraction of the eluate flow is split and introduced through a narrow orifice or diaphragm directly into the ion source, with solvent-mediated chemical ionization. This interface was largely superseded by atmospheric pressure ionization methods.
A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments.
OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state.
This child of the former purgatory term ion chemical type was made obsolete.
OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion.
A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons.
A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time.
An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa.
OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion.
high-field asymmetric waveform ion mobility spectrometry
The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization.
The removal of electrons from any species by interaction with a high electric field.
The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas.
OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
A device for spatially confining ions using electric and magnetic fields alone or in combination.
OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393).
OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process.
mass analyzed ion kinetic energy spectrometry
OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
This child of the former purgatory term m/z Separation Method was made obsolete.
Chemical ionization that results in the formation of negative ions.
With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species.
neutralization reionization mass spectrometry
The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended.
A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source.
A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation.
Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species.
resonance enhanced multiphoton ionization
OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber.
The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization.
surface enhanced laser desorption ionization
Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
This term was made obsolete because it was replaced by surface ionization (MS:1000406).
A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions.
A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time.
OBSOLETE Mass spectrometry using spark ionization.
This term was made obsolete because it was replaced by spark ionization (MS:1000404).
A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments.
stored waveform inverse fourier transform
The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum.
Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse.
OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
A device that uses an oscillating electric field and magnetic field to accelerate charged particles.
OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam.
OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry.
A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap.
OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate.
OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions.
A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z).
OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians.
OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians.
OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected.
This term was made obsolete because it is redundant to quadrupole ion trap.
OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path.
OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term.
A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time.
OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection.
OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry.
OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
transmission quadrupole mass spectrometer
The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB.
OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time.
Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle.
The magnitude of the force per unit charge at a given point in space.
The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole.
The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element.
A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field.
OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer.
OBSOLETE The limit of m/z over which a mass spectrometer can detect ions.
OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap.
OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap.
OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer.
OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage.
OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it.
The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time.
An electric or magnetic field that does not change in time.
OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained.
The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z.
OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement.
OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment.
A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell.
A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244).
A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions.
OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum.
OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors.
This child of the former purgatory term linked scan was made obsolete.
OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan records a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors.
OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended.
OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan.
Linked Scan at Constant B[1-(E/E0)]^1/2 / E
OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discrete steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.
OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition.
The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type).
OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated.
This child of the former purgatory term product ion was made obsolete.
OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.
OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions.
This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated.
This child of the former purgatory term ion role was made obsolete.
Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z.
OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated.
OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions.
OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+.
Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector.
A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected.
One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode.
A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier.
A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially.
A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector.
OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go.
Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules.
OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure.
OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+.
OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic.
OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used.
OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-.
OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion.
OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives.
OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+.
OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion.
OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions.
OBSOLETE A product ion that results from the dissociation of a precursor ion.
This term was made obsolete because it was replaced by product ion (MS:1000342).
OBSOLETE An atomic or molecular species having a net positive or negative electric charge.
OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue.
OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer.
OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection.
This child of the former purgatory term ion stability type was made obsolete.
OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion.
OBSOLETE An atomic or molecular species having a net negative electric charge.
OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions.
OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+.
OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions.
OBSOLETE An atomic or molecular species having a net positive electric charge.
OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended.
OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation.
OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion.
OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer.
OBSOLETE An ion with sufficient energy to dissociate within the ion source.
A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state.
An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron.
Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source.
The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source.
The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization.
The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization.
The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface.
The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion.
The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules.
OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products.
The ratio of the number of ions formed to the number of electrons, molecules or photons used.
The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing.
The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization.
A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source.
Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray.
Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potential on the tip of the electrospray needle and/or a gas pressure to push the sample through the needle. See also electrospray ionization and microelectrospray.
Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited.
OBSOLETE An electronic state capable of undergoing auto-Ionization.
The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions.
The formation of gas-phase ions without extensive fragmentation.
The formation of ions from a solid material by an intermittent electrical discharge.
The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization.
surface-assisted laser desorption ionization
The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
The ionization of a neutral species through contact with a high temperature surface.
A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state.
OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion.
OBSOLETE A homolytic cleavage where the bond fission occurs between the atom adjacent to the atom at the apparent charge site and an atom removed from the apparent charge site by two bonds.
OBSOLETE A homolytic cleavage where the bond fission occurs between an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the apparent charge site by three bonds.
An inert gas used for collisional deactivation of internally excited ions.
OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation.
OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion.
OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion.
OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion.
OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species.
OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion.
An inert gas used for collisional excitation. The term target gas is not recommended.
OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis.
OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV.
A collision-induced dissociation process that occurs in a beam-type collision cell.
beam-type collision-induced dissociation
OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis.
OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer.
OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species.
OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral.
OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule.
OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions.
OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants.
OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product.
OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account.
OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower.
A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative.
low-energy collision-induced dissociation
OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied.
A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral.
OBSOLETE Chemical transformation involving an ion.
This child of the former purgatory term ion was made obsolete.
OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners.
OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion.
OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion.
Function or process of the mass spectrometer where it records a spectrum.
Representation of intensity values corresponding to a range of measurement space.
Mass analyzer separates the ions according to their mass-to-charge ratio.
OBSOLETE Sequential m/z separation method.
The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample.
Terms used to describe types of data processing.
OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5.
Ion selection properties that are associated with a value.
Terms to describe the precursor activation.
OBSOLETE Terms used to describe the spectrum.
This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000).
Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions.
Description of the instrument or the mass spectrometer.
OBSOLETE A unit of measurement for mass.
This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002).
Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer.
The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2.
The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications.
The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition.
The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges.
The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration.
The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor.
OBSOLETE Terms that will likely become obsolete unless there are wails of dissent.
The whole branch purgatory term was made obsolete.
Analyzer properties that are associated with a value.
Detector attribute recognized as a value.
Property of a source device that need a value.
Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific.
Thermo Fisher Scientific instrument model
An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer.
Potential difference at the MS source in volts.
Ion optics involves components that help focus ion streams in mass spectrometry.
Thermo Electron Corporation instrument model.
Instrument properties that are associated with a value.
Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.
Nonphysical characteristic attributed to a spectrum.
The upper m/z bound of a mass spectrometer scan window.
The lower m/z bound of a mass spectrometer scan window.
The time spent gathering data across a peak.
Nonphysical characteristic attributed to a spectrum acquisition scan.
M/z value of the signal of highest intensity in the mass spectrum.
The intensity of the greatest peak in the mass spectrum.
Nonphysical characteristic attributed to an ion.
Stage number achieved in a multi stage mass spectrometry acquisition.
A string unique to Thermo instrument describing instrument settings for the scan.
Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float.
32-bit precision little-endian floating point conforming to IEEE-754.
64-bit precision little-endian floating point conforming to IEEE-754.
Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks.
Waters data file format found in a Waters RAW directory, generated from an MS acquisition.
Highest m/z value observed in the m/z array.
Lowest m/z value observed in the m/z array.
Conversion of one file format to another.
Software related to the recording or transformation of spectra.
Thermo Finnigan software for data acquisition and analysis.
Thermo Finnigan software for data analysis of peptides and proteins.
Micromass software for data acquisition and analysis.
Applied Biosystems software for data acquisition and analysis.
A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology.
Applied Biosystems MALDI-TOF data acquisition and analysis system.
Voyager Biospectrometry Workstation System
A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw".
A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program.
Data processing attribute used to describe the type of data processing performed on the data file.
Conversion of a file format to Proteomics Standards Initiative mzML file format.
Conversion of a file format to Institute of Systems Biology mzXML file format.
Conversion of a file format to Proteomics Standards Initiative mzData file format.
Sample properties that are associated with a value.
Selection window properties that are associated with a value.
This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003).
SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition.
A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.
The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
Proteomics Standards Initiative mzData file format.
Institute of Systems Biology mzXML file format.
MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files.
SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard.
Method used to combine the mass spectra.
Spectra is combined by calculating the median of the spectra.
Spectra is combined by calculating the mean of the spectra.
Data file from which an entity is sourced.
Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n.
multiple-stage mass spectrometry spectrum
Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
Proteomics Standards Initiative mzML file format.
Details about a person or organization to contact in case of concern or discussion about the file.
Name of the contact person or organization.
Postal address of the contact person or organization.
Uniform Resource Locator related to the contact person or organization.
Email address of the contact person or organization.
A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program.
A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process.
A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparison between intensities of m/z values.
The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
A data array of relative time offset values from a reference time.
A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions.
A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected.
Database application and analysis platform for proteomics.
Shimadzu Scientific Instruments instrument model.
Shimadzu Scientific Instruments LCMS-IT-TOF MS.
Shimadzu Scientific Instruments LCMS-2010EV MS.
Shimadzu Scientific Instruments LCMS-2010A MS.
Shimadzu Biotech AXIMA CFR MALDI-TOF MS.
Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS.
Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS.
Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS.
Peak list file format used by ProteinLynx Global Server.
ProteinLynx Global Server mass spectrum XML format
ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time.
A data array of electromagnetic radiation wavelength values.
Highest wavelength observed in an EMR spectrum.
Lowest wavelength observed in an EMR spectrum.
OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum).
This term was made obsolete because it was replaced by absorption spectrum (MS:1000806).
An array detector used to record spectra in the ultraviolet and visible region of light.
Representation of a chromatographic separation attribute measurement versus time.
Type of chromatogram measurement being represented.
Representation of an array of the measurements of a specific single ion current versus time.
Representation of an array of the most intense peaks versus time.
Threshold below which some action is taken.
Data processing parameter used in the data processing performed on the data file.
Threshold above which some action is taken.
A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty.
Thermo Scientific LTQ Orbitrap XL MS with ETD.
Thermo Scientific MALDI LTQ Orbitrap MS.
Thermo Scientific TSQ Quantum Access MS.
Thermo Scientific Element GD Glow Discharge MS.
Thermo Scientific GC IsoLink Isotope Ratio MS.
Thermo Scientific software for data analysis of peptides and proteins.
SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200.
SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer.
SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS.
SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS.
SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite.
Applied Biosystems|MDS SCIEX QSTAR Pulsar.
Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer.
SCIEX or Applied Biosystems software for data acquisition and analysis.
Waters Corporation Xevo MRT Mass Spectrometer.
SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.
SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.
Applied Biosystems|MDS SCIEX software for tissue imaging.
Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling.
Applied Biosystems|MDS SCIEX software for MRM assay development.
Applied Biosystems|MDS SCIEX software for bio-related data exploration.
Applied Biosystems|MDS SCIEX software for protein identification.
Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT.
Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ.
Applied Biosystems|MDS SCIEX software for MS-BLAST identification.
SCIEX Cliquid software for data analysis and quantitation.
Applied Biosystems|MDS SCIEX software for MRM-based quantitation.
The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
Software for data acquisition of 6000 series instruments.
Software for open access data acquisition.
Software for data analysis of data from 6000 series instruments.
Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data.
Software for identification of metabolites.
Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites.
Software for protein identification and characterization of complex protein digest mixtures.
Spectrum Mill for MassHunter Workstation
Software for data analysis of 6300 series ion trap mass spectrometers.
6300 Series Ion Trap Data Analysis Software
Agilent software for data acquisition and analysis.
Applied Biosystems|MDS SCIEX software for data acquisition and analysis.
Bruker software for data acquisition and analysis.
Waters software for data acquisition and analysis.
Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
Bruker Daltonics' autoflex III smartbeam: MALDI TOF.
Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI.
Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR.
Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD.
Bruker Daltonics' microflex LT: MALDI TOF.
Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI.
Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI.
Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI.
Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF.
Bruker Compass for HCT/esquire software.
Bruker stand-alone software for data conversion.
Bruker software library for data access.
Parameter file used to configure the acquisition of raw data on the instrument.
Mass-to-charge ratio of an selected ion.
The correction of the spectrum scan times, as used e.g. in label-free proteomics.
The removal of very high intensity data points.
The time that a data processing action was finished.
TOPP (The OpenMS proteomics pipeline) software.
Removes the baseline from profile spectra using a top-hat filter.
Exports data from an OpenMS database to a file.
Converts between different MS file formats.
Extracts or manipulates portions of data from peak, feature or consensus feature files.
OBSOLETE Corrects retention time distortions between maps.
This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch.
Normalizes peak intensities in an MS run.
OBSOLETE Removes noise from profile spectra by using different smoothing techniques.
This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch.
OBSOLETE Finds mass spectrometric peaks in profile mass spectra.
This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch.
Transforms an LC/MS map into a resampled map or a png image.
OBSOLETE Applies a filter to peak spectra.
This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch.
Describes how the native spectrum identifiers are formatted.
Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger.
Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger.
Native format defined by scan=xsd:nonNegativeInteger.
Native format defined by file=xsd:IDREF.
The nativeID must be the same as the source file ID.
Native format defined by index=xsd:nonNegativeInteger.
Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
Native format defined by spectrum=xsd:nonNegativeInteger.
Used for conversion from mzData. The spectrum id attribute is referenced.
A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm.
Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z.
below precursor intensity dominance charge state calculation
A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions.
Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans.
Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques.
Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible.
Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added.
Threshold at or below which some action is taken.
Threshold at or above which some action is taken.
MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions.
MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation.
This term was made obsolete because it was merged with zoom scan (MS:1000497).
OBSOLETE The highest m/z being isolated in an isolation window.
This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
OBSOLETE The lowest m/z being isolated in an isolation window.
Use this term if only one scan was recorded or there is no information about scans available.
Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file.
This is the preferred storage place for the spectrum TITLE from an MGF peak list.
A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.
A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.
A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added.
The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported.
Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported.
Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported.
Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value.
A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited.
A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited.
Unit describing the scan rate of a spectrum in Thomson per second.
Chromatogram properties that are associated with a value.
A free-form text title describing a chromatogram.
This is the preferred storage place for the spectrum title.
Representation of the current of ions versus time.
Representation of electromagnetic properties versus time.
Representation of light absorbed by the sample versus time.
Representation of light emitted by the sample versus time.
The number of counted events observed per second in one or a group of elements of a detector.
Bruker software for hyphenated experiments.
A data array of temperature measurements.
Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format.
The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography.
The primary or reference m/z about which the isolation window is defined.
The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation.
See MS:1000014 for the related term of accuracy.
Properties of the preparation steps which took place before the measurement was performed.
Attributes to describe the technique how the sample is prepared with the matrix solution.
Describes the technique how the matrix is put on the sample target.
Describes the chemical solution used as matrix.
Concentration of the chemical solution used as matrix.
Dried droplet in MALDI matrix preparation.
Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation.
Laser properties that are associated with a value.
Type of laser used for desorption purpose.
OBSOLETE The distance between two peaks of the emitted laser beam.
This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242).
Describes the diameter of the laser beam in x direction.
Describes the diameter of the laser beam in y direction.
Describes output energy of the laser system. May be attenuated by filters or other means.
Describes how long the laser beam was emitted from the laser device.
Describes the reduction of the intensity of the laser beam energy.
Describes the angle between the laser beam and the sample target.
Laser which is powered by a gaseous medium.
Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states.
Dye lasers use an organic dye as the gain medium.
Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term.
Thermo Scientific LTQ Velos MS with ETD.
Identifier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information.
Group of two or more atoms held together by chemical bonds.
A molecule of low molecular weight that is composed of two or more amino acid residues.
A physical characteristic of a molecular entity.
The pH of a solution at which a charged molecule does not migrate in an electric field.
The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
A combination of symbols used to express the chemical composition of a molecule.
A chemical formula which expresses the proportions of the elements present in a substance.
A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
The gas pressure of the collision gas used for collisional excitation.
OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.
This term was obsoleted because was redundant to MS:1000139.
Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.
Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
Software used to predict or calculate numerical attributes of peptides.
Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence.
Potential difference between the orifice and the skimmer in volts.
Potential difference between the sampling cone/orifice in volts.
Potential difference setting of the tube lens in volts.
An identifier/accession number to an external reference database.
A unique identifier for a publication in the PubMed database (MIR:00000015).
The duration of intervals between scanning, during which the instrument configuration is switched.
Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene.
A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
A nonphysical characteristic attributed to a specific protein.
Identifier for a specific protein in a database.
A long name describing the function of the protein.
Nonphysical characteristic attributed to a peptide.
Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away.
Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present.
Make it more general as there are actually many other ways to display a modified peptide sequence.
A state description of how a peptide might be isotopically or isobarically labelled.
A peptide that has been created or labelled with some heavier-than-usual isotopes.
A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
A time interval from the start of chromatography when an analyte exits a chromatographic column.
A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup.
A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup.
A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application.
Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column.
The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column.
H-PINS retention time normalization standard
The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion).
The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z.
The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries.
Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc.
Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitable peak is 2, etc. Suitability is algorithm and context dependent.
A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely.
The strategy used to validate that a transition is effective.
The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined.
transition optimized on specified instrument
The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term.
transition validated with an MS/MS spectrum on specified instrument
The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad).
transition purported from an MS/MS spectrum on a different, specified instrument
The transition has been predicted by informatics software without any direct spectral evidence.
transition predicted by informatic analysis
A file format that has two or more columns of tabular data where each column is separated by a TAB character.
An attribute of a window in time about which a peptide might elute from the column.
The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time.
The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time.
A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically.
A priority setting specifying whether included or excluded targets have priority over the other.
A priority setting specifying that included targets have priority over the excluded targets if there is a conflict.
A priority setting specifying that excluded targets have priority over the included targets if there is a conflict.
Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington.
Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.
OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
This term was made obsolete because it was redundant with an existing term (MS:1000872).
Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology.
The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1.
The length of time spent filling an ion trapping device.
A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample.
Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger.
Applied Biosystems|MDS SCIEX QTRAP 5500.
SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer.
Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
Name of the gene from which the protein is translated.
The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra.
Number of full protein descriptions to show for top N peptides.
A de novo sequencing search (without database).
The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).
The name of the search database (nr, SwissProt or est_human).
OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view.
URI, from where the search database was originally downloaded.
Version of the search database. In mzIdentML use the attribute instead.
Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term.
Database containing amino acid or nucleic acid sequences.
Was there filtering used on the database.
A taxonomy filter was to the database search.
Filtering applied specifically by accession number pattern.
Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value.
Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value.
The translated open reading frames from a nucleotide database considered in the search (range: 1-6).
The translation table used to translate the nucleotides to amino acids.
Filtering applied specifically by amino acid sequence pattern.
String in the header of a sequence entry for that entry to be searched.
The number of sequences (proteins / nucleotides) from the database search after filtering.
Number of peptide seqs compared to each spectrum.
OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run.
The time taken to complete the search in seconds.
Flag indicating that fragment ions should be shown.
Type of the source file, the mzIdentML was created from.
Specify "number of dtas shown" as value of the CVParam.
Sort order of SEQUEST search results by the delta of the normalized correlation score.
Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M.
Sort order of SEQUEST search results given by the ions.
Sort order of SEQUEST search results given by the mass of the protonated ion.
Sort order of SEQUEST search results given by the probability.
OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any.
Sort order of SEQUEST search results given by the previous amino acid.
Sort order of SEQUEST search results given by the reference.
Modification parameters for the search engine run.
The specificity rules for the modifications applied by the search engine.
The quality estimation was done manually.
Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide).
Method for quality estimation (manually or with decoy database).
OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD.
OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms.
This term was made obsolete and is replaced by the term (MS:1001961).
The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine.
Sort order of SEQUEST search results by the Sp score.
Sort order of SEQUEST search results given by the total ion current.
Sort order of SEQUEST search results given by the scan number.
Sort order of SEQUEST search results given by the sequence.
Sort order of SEQUEST search results given by the SEQUEST result 'Sf'.
Database contains nucleic acid sequences.
Enumeration of type of search value (i.e. from PMF, sequence tag, MS2).
Non-redundant GenBank sequence database.
Sort order of SEQUEST search results by the correlation score.
SEQUEST View / Process Input Parameters.
The protein description line from the sequence entry in the source database FASTA file.
The taxonomy of the resultant molecule from the search.
OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT).
This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956).
Identification confidence metric for a peptide.
peptide sequence-level identification statistic
The percent coverage for the protein based upon the matched peptide sequences (can be calculated).
Sort order of SEQUEST search results given by the charge.
Specify "percentage" as value of the CVParam.
This counts distinct sequences hitting the protein without regard to a minimal confidence threshold.
This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere.
The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than.
This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere.
The name of the UniProtKB/Swiss-Prot knowledgebase.
peptide sequence-level identification attribute
Specify "number" as value of the CVParam.
Source file for this mzIdentML was a data set in a database.
Parameter information, type of product: a ion with charge on the N-terminal side.
Specify cull string as value of the CVParam.
Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.
Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.
OBSOLETE Retention time of the spectrum from the source file.
This term was made obsolete because scan start time (MS:1000016) should be used instead.
OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData.
Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group).
The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
Parameter information, type of product: b ion with charge on the N-terminal side.
Parameter information, type of product: c ion with charge on the N-terminal side.
The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count.
The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb).
The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't.
The number of peaks from the original peaks listed that were submitted to the search engine.
Result of quality estimation: decision of a manual validation.
Accessions Containing Sequence - Accessions for each protein containing this peptide.
This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).
OBSOLETE P-value (protein diff from 1 randomly).
This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).
Absolute quantity in terms of real concentration or molecule copy number in sample.
This term was made obsolete because part of mzQuantML schema.
International Protein Index database for Homo sapiens sequences.
Search engine specific peptide spectrum match scores.
PSM-level search engine specific statistic
SEQUEST Select Advanced Input Parameters.
Ion a-NH3 parameter information, type of product: a ion with lost ammonia.
Ion a-H2O if a significant and fragment includes STED.
Ion b-NH3 parameter information, type of product: b ion with lost ammonia.
Ion b-H2O if b significant and fragment includes STED.
Ion y-NH3 parameter information, type of product: y ion with lost ammonia.
This term was made obsolete - use MS:1001262 and MS:1002455 instead.
The Paragon result 'Expression Error Factor'.
The Paragon result 'Expression change P-value'.
Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search.
number of molecular hypothesis considered
Expressed sequence tag nucleotide sequence database.
Regular expressions for cleavage enzymes.
The details of the actual run of the search.
Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
As parameter for search engine: apply the modification only at the N-terminus of a peptide.
As parameter for search engine: apply the modification only at the C-terminus of a peptide.
This term was made obsolete because now is split into peptide and protein terms.
Result of quality estimation: Expect value.
Result of quality estimation: confidence score.
Decoy type: Amino acids of protein sequences are used in reverse order.
Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass).
Decoy database composition: database contains original (target) and decoy entries.
Identification confidence metric for a protein.
protein identification confidence metric
Source file for this mzIdentML was in Mascot DAT file format.
Source file for this mzIdentML was in SEQUEST out file format.
Maximum value of molecular weight filter.
Minimum value of molecular weight filter.
Maximum value of isoelectric point filter.
Minimum value of isoelectric point filter.
The type of mass difference value to be considered by the search engine (monoisotopic or average).
Mass type setting for parent mass was monoisotopic.
Mass type setting for parent mass was average isotopic.
OBSOLETE: Scores and global result characteristics.
Estimation of the global false discovery rate of proteins.
The SEQUEST result 'Sp' in out file (peptide).
The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'.
The SEQUEST result '#' in out file (peptide).
The SEQUEST result 'Id#' in out file (peptide).
Fragmentation information, type of product: y ion.
Fragmentation information like ion types.
Fragmentation information, type of product: b ion without water.
Fragmentation information, type of product: y ion without water.
Fragmentation information, type of product: b ion.
Fragmentation information, type of product: x ion.
Fragmentation information, type of product: a ion.
Fragmentation information, type of product: z ion.
Fragmentation information, type of product: c ion.
Ion b-NH3 fragmentation information, type of product: b ion without ammonia.
Ion y-NH3 fragmentation information, type of product: y ion without ammonia.
Fragmentation information, type of product: a ion without water.
Ion a-NH3 fragmentation information, type of product: a ion without ammonia.
Fragmentation information, type of product: d ion.
Fragmentation information, type of product: v ion.
Fragmentation information, type of product: w ion.
Fragmentation information, type of product: immonium ion.
Source file for this mzIdentML was a SEQUEST folder with its out files.
Source file for this mzIdentML was a SEQUEST summary page (proteins).
Result of quality estimation: the local FDR at the current position of a sorted list.
Mass type setting for fragment mass was average isotopic.
Mass type setting for fragment mass was monoisotopic.
Parameter information, type of product: side chain loss v ion.
Parameter information, type of product: side chain loss d ion.
Parameter information, type of product: immonium ion.
Parameter information, type of product: side chain loss w ion.
Parameter information, type of product: x ion with charge on the C-terminal side.
Parameter information, type of product: y ion with charge on the C-terminal side.
Parameter information, type of product: z ion with charge on the C-terminal side.
Source data for this mzIdentML was a ProteinScape SearchEvent.
Source data for this mzIdentML was a ProteinScape Gel.
Specify the regular expression for decoy accession numbers.
OBSOLETE The name of the database, the search database was derived from.
This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
International Protein Index database for Mus musculus sequences.
International Protein Index database for Rattus norvegicus sequences.
International Protein Index database for Danio rerio sequences.
International Protein Index database for Gallus gallus sequences.
International Protein Index database for Bos taurus sequences.
International Protein Index database for Arabidopsis thaliana sequences.
OBSOLETE Decoy database from a non-redundant GenBank sequence database.
OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus.
OBSOLETE Decoy database from a International Protein Index database for Mus musculus.
OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana.
OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database.
OBSOLETE Decoy database from a International Protein Index database for Danio rerio.
OBSOLETE Decoy database from a Swiss-Prot protein sequence database.
OBSOLETE Decoy database from a International Protein Index database for Gallus gallus.
OBSOLETE Decoy database from a International Protein Index database for Bos taurus.
OBSOLETE Decoy database from a International Protein Index database for Homo sapiens.
The rank of the protein in a list sorted by the search engine.
Search engine specific input parameters.
Enzyme Asp-N, Ammonium Bicarbonate (AmBic).
Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05).
The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1.
Mascot protein scoring method; either 'Standard' or 'MudPIT'.
Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed.
If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed.
If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed.
Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits.
If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use.
If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included.
If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database.
Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data.
Details about a single database sequence.
The sequence is a nucleic acid sequence.
Children of this term specify the source of the mass table used.
The masses used in the mass table are taken from AAIndex.
The children of this term define file formats of the sequence database used.
The sequence database was stored in the FASTA format.
The sequence database was stored in the Abstract Syntax Notation 1 format.
The sequence database was stored in the NCBI formatdb (*.p*) format.
ClustalW ALN (multiple alignment) format.
Root node for options for the mass table used.
Description of the quality of the input spectrum.
This term reports the quality of the spectrum assigned by msmsEval.
Children of this term describe ambiguous residues.
List of standard residue one letter codes which are used to replace a non-standard.
List of masses a non-standard letter code is replaced with.
Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
Fragmentation information, type of product: internal yb ion.
Fragmentation information, type of product: internal ya ion.
Fragmentation information, type of product: z+1 ion.
Fragmentation information, type of product: z+2 ion.
Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search.
The instrument type parameter value in Phenyx.
The default parent charge value in Phenyx.
The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct.
The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx.
The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx.
The list of ion series considered in the turbo mode of Phenyx.
The minimal number of residues for a peptide to be considered for a valid identification in Phenyx.
The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx.
The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx.
The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx.
The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used.
The primary sequence database identifier of a protein in Phenyx.
A secondary sequence database identifier of a protein in Phenyx.
The protein score of a protein match in Phenyx.
First number of phenyx result "#Peptides".
Second number of phenyx result "#Peptides".
The value of the automatic peptide acceptance filter in Phenyx.
The value of the user-defined peptide acceptance filter in Phenyx.
The z-score value of a peptide sequence match in Phenyx.
The p-value of a peptide sequence match in Phenyx.
The number of missed cleavages of a peptide sequence in Phenyx.
The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx.
Source file for this mzIdentML was in OMSSA csv file format.
Source file for this mzIdentML was in OMSSA xml file format.
Source file for this mzIdentML was in X!Tandem xml file format.
This subsection describes terms which can describe details of spectrum identification results.
Parameter information, type of product: internal yb ion.
Parameter information, type of product: internal ya ion.
Parameter information, type of product: z+1 ion.
Parameter information, type of product: z+2 ion.
The translation start codons used to translate the nucleotides to amino acids.
OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file.
OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file.
OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE.
SpectraST dot product of two spectra, measuring spectral similarity.
SpectraST measure of how much of the dot product is dominated by a few peaks.
SpectraST normalised difference between dot product of top hit and runner-up.
The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers.
The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers.
A URL that describes the translation table used to translate the nucleotides to amino acids.
Name of the used method in the ProteinExtractor algorithm.
Flag indicating if a non redundant scoring should be generated.
Flag indicating if identified proteins should be included.
The maximum number of proteins to consider.
The maximum considered mass for a protein.
The minimum number of proteins to consider.
Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score.
Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score.
In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation.
Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score.
Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score.
In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation.
Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score.
Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score.
In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation.
Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score.
Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score.
In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation.
Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
False-discovery rate threshold for proteins.
False-discovery rate threshold for peptides.
Threshold for OMSSA e-value for quality estimation.
Details of decoy generation and database structure.
Name of algorithm used for decoy generation.
Decoy type: Amino acids of protein sequences are used in a random order.
Decoy database composition: database contains only decoy entries.
Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy).
quality estimation with implicit decoy sequences
Vocabularies describing the spectrum generation information.
This term should be given if the modification was unknown.
The sequence database was stored in the PEFF (PSI enhanced FastA file) format.
This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens.
This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
The children of this term can be used to describe modifications.
Representation of an array of the measurements of a selectively monitored ion versus time.
Representation of an array of the measurements of a selectively monitored reaction versus time.
selected reaction monitoring chromatogram
OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time.
This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way.
consecutive reaction monitoring chromatogram
Open Mass Spectrometry Search Algorithm was used to analyze the spectra.
X!Tandem was used to analyze the spectra.
Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline.
Mascot Parser was used to analyze the spectra.
Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte.
Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger.
Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database.
SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis.
Normalization of data point intensities.
Calibration of data point m/z positions.
An algorithm for protein determination/assembly integrated into Bruker's ProteinScape.
The SearchResultId of this peptide as SearchResult in the ProteinScape database.
The SearchEventId of the SearchEvent in the ProteinScape database.
The Profound probability score stored by ProteinScape.
The ProteinSolver exp value stored by ProteinScape.
The ProteinSolver score stored by ProteinScape.
The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape.
The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores.
The score calculated by ProteinExtractor.
Native format defined by scanId=xsd:nonNegativeInteger.
A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer.
Filter types which are used to filter a sequence database.
Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search.
Fragmentation information, type of product: c ion without water.
Fragmentation information, type of product: c ion without ammonia.
Fragmentation information, type of product: z ion without water.
Fragmentation information, type of product: z ion without ammonia.
Fragmentation information, type of product: x ion without water.
Fragmentation information, type of product: x ion without ammonia.
Fragmentation information, type of product: precursor ion without water.
Fragmentation information, type of product: precursor ion without ammonia.
Fragmentation information, type of product: precursor ion.
This term can describe a neutral loss m/z value that is lost from an ion.
Native format defined by databasekey=xsd:long.
A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier).
spectrum from database integer nativeID format
Spectra from Bruker/Protagen Proteinscape database.
Native format defined by query=xsd:nonNegativeInteger.
The spectrum (query) number in a Mascot results file, starting from 1.
Child-terms contain information to map the results back to spectra.
Native format defined by mzMLid=xsd:IDREF.
A unique identifier of a spectrum stored in an mzML file.
A unique identifier of a spectrum stored in a ProteinScape database.
spectrum from ProteinScape database nativeID format
Native format defined by databasekey=xsd:string.
spectrum from database string nativeID format
Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional).
Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI.
Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI.
Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR.
Bruker Daltonics' microflex LRF: MALDI TOF.
Bruker Daltonics' ultrafleXtreme: MALDI TOF.
Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR.
Bruker Daltonics' microflex II: MALDI TOF.
Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF.
Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF.
Shimadzu Biotech software for data acquisition, processing, and analysis.
Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format.
Source file for this mzIdentML was in SEQUEST SQT format.
Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format.
Source file for this mzIdentML was in Waters IdentityE XML format.
Source file for this mzIdentML was in Waters ProteinLynx XML format.
Source file for this mzIdentML was in Agilent SpectrumMill directory format.
Flag indicating to report only the spectra assigned to identified proteins.
report only spectra assigned to identified proteins
Minimum number of peptides a protein must have to be accepted.
Minimum protein probability a protein must have to be accepted.
Minimum probability a peptide must have to be accepted for protein scoring.
Minimum number of enzymatic termini a peptide must have to be accepted.
Discriminant score from Agilent SpectrumMill software.
The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.
MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.
Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF).
Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.
Tabb Lab software for generating sequence tags from tandem mass spectra.
Tabb Lab software for reconciling sequence tags to a protein database.
Tabb Lab software for spectral library searches on tandem mass spectra.
Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
A representative protein selected from a set of sequence same-set or spectrum same-set proteins.
A protein with significant homology to another protein, but some distinguishing peptide matches.
TO ENDETAIL: a really generic relationship OR ortholog protein.
group member with undefined relationship OR ortholog protein
A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences.
A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra.
A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches.
A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches.
A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins.
A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins.
Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable).
OBSOLETE Name and location of the .raw file or files.
This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
ProteomeDiscoverer:Spectrum Files:Raw File names
OBSOLETE Path and name of the .srf (SEQUEST Result Format) file.
This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
ProteomeDiscoverer:SRF File Selector:SRF File Path
OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc).
This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead.
ProteomeDiscoverer:Spectrum Selector:Ionization Source
OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any).
This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead.
ProteomeDiscoverer:Spectrum Selector:Lower RT Limit
OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS).
This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead.
Maximum mass limit of a singly charged precursor ion.
Minimum mass limit of a singly charged precursor ion.
Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow.
ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
OBSOLETE Level of the mass spectrum (MS2 ... MS10).
This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
OBSOLETE Polarity mode (positive or negative).
This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead.
Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3).
ProteomeDiscoverer:Spectrum Selector:Precursor Selection
Signal-to-Noise ratio below which peaks are removed.
OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)).
This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead.
Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value.
ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header.
ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements
Specifies the charge state of the precursor ions, if it is not defined in the scan header.
ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements
Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header.
ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements
Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header.
ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements
Specifies the polarity of the ions monitored if it is not included in the scan header.
ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements
ProteomeDiscoverer:Spectrum Selector:Upper RT Limit
Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors.
ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset
ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass
Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed.
ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor
Determines whether neutral loss peaks are removed from ETD and ECD spectra.
ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks
Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra.
ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses
Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum.
ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones
Determines whether precursor artifact peaks from the MS2 input spectra are removed.
ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak
Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type.
ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch
Determines whether spectra from different MS order scans can be grouped together.
ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch
OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species.
This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead.
ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis.
ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion
Highest charge state that is allowed for the deconvolution of multiply charged data.
ProteomeDiscoverer:Xtract:Highest Charge
OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead.
Lowest charge state that is allowed for the deconvolution of multiply charged data.
OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead.
Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum.
ProteomeDiscoverer:Xtract:Monoisotopic Mass Only
Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted).
ProteomeDiscoverer:Xtract:Overlapping Remainder
Accuracy required for a pattern fit to be considered valid.
ProteomeDiscoverer:Xtract:Required Fitting Accuracy
ProteomeDiscoverer:Xtract:Resolution At 400
Minimum charge state below which peptides are filtered out.
Maximum charge above which peptides are filtered out.
Determines whether spectra with scores above the threshold score are retained rather than filtered out.
ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores
Determine dynamic post-translational modifications (PTMs).
Static Modification to all occurrences of a named amino acid.
OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database.
This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead.
Determines whether to search error-tolerant.
ProteomeDiscoverer:Mascot:Error tolerant Search
Maximum size of the .mgf (Mascot Generic Format) file in MByte.
ProteomeDiscoverer:Mascot:Max MGF File Size
URL (Uniform resource Locator) of the Mascot server.
ProteomeDiscoverer:Mascot:Mascot Server URL
Number of attempts to submit the Mascot search.
ProteomeDiscoverer:Mascot:Number of attempts to submit the search
ProteomeDiscoverer:Mascot:X Static Modification
OBSOLETE Name of the user submitting the Mascot search.
This term was made obsolete because it's recommended to use researcher (MS:1001271) instead.
Time interval between attempts to submit a search in seconds.
ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search
OBSOLETE Specifies the enzyme reagent used for protein digestion.
This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead.
OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu.
This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead.
ProteomeDiscoverer:Fragment Mass Tolerance
Type of instrument used to acquire the data in the raw file.
Maximum number of missed cleavage sites to consider during the digest.
ProteomeDiscoverer:Maximum Missed Cleavage Sites
Minimum score in the IonScore column that each peptide must exceed in order to be reported.
ProteomeDiscoverer:Mascot:Peptide CutOff Score
OBSOLETE Mass window for which precursor ions are considered to be the same species.
ProteomeDiscoverer:Precursor Mass Tolerance
Minimum protein score in the IonScore column that each protein must exceed in order to be reported.
ProteomeDiscoverer:Mascot:Protein CutOff Score
OBSOLETE Database to use in the search (configured on the Mascot server).
This term was made obsolete because it's recommended to use database name (MS:1001013) instead.
Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report.
ProteomeDiscoverer:Mascot:Protein Relevance Factor
Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence.
Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence.
OBSOLETE Limits searches to entries from a particular species or group of species.
This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead.
OBSOLETE Use average mass for the precursor.
This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead.
ProteomeDiscoverer:Use Average Precursor Mass
OBSOLETE Determines whether to use MudPIT or normal scoring.
This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead.
Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported.
ProteomeDiscoverer:Absolute XCorr Threshold
Determines whether to calculate a probability score for every peptide match.
ProteomeDiscoverer:SEQUEST:Calculate Probability Score
Dynamic C-terminal modification that is used during the search.
ProteomeDiscoverer:SEQUEST:CTerminal Modification
Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained.
ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage
Maximum number of identical modifications that a single peptide can have.
ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide
Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance.
ProteomeDiscoverer:Max Modifications Per Peptide
Maximum number of peptides that are searched and scored per spectrum.
ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered
Maximum number of peptide matches reported per spectrum.
ProteomeDiscoverer:Maximum Peptides Output
Maximum number of proteins that a single identified peptide can be associated with during protein assembly.
ProteomeDiscoverer:Maximum Protein References Per Peptide
Dynamic N-terminal modification that is used during the search.
ProteomeDiscoverer:SEQUEST:NTerminal Modification
Static modification for the C terminal of the peptide used during the search.
Static modification for the N terminal of the peptide used during the search.
Specifies a factor to apply to the protein score.
ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor
Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report.
ProteomeDiscoverer:Protein Relevance Threshold
OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database.
ProteomeDiscoverer:Search Against Decoy Database
ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses
Determines whether a ions with neutral loss are used for spectrum matching.
ProteomeDiscoverer:Use Neutral Loss a Ions
Determines whether b ions with neutral loss are used for spectrum matching.
ProteomeDiscoverer:Use Neutral Loss b Ions
Determines whether y ions with neutral loss are used for spectrum matching.
ProteomeDiscoverer:Use Neutral Loss y Ions
Determines whether z ions with neutral loss are used for spectrum matching.
ProteomeDiscoverer:Use Neutral Loss z Ions
Uses a ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of a Ions
Uses b ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of b Ions
Uses c ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of c Ions
ProteomeDiscoverer:SEQUEST:Weight of d Ions
ProteomeDiscoverer:SEQUEST:Weight of v Ions
ProteomeDiscoverer:SEQUEST:Weight of w Ions
Uses x ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of x Ions
Uses y ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of y Ions
Uses z ions for spectrum matching with this relative factor.
ProteomeDiscoverer:SEQUEST:Weight of z Ions
Sets a minimum protein score that each protein must exceed in order to be reported.
ProteomeDiscoverer:ZCore:Protein Score Cutoff
Specifies which peak to select if more than one peak is found inside the integration window.
ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method
Specifies the mass-to-charge window that enables one to look for the reporter peaks.
ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance
Quantitation method for isobarically labeled quantitation.
ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method
OBSOLETE Format of the exported spectra (dta, mgf or mzData).
ProteomeDiscoverer:Spectrum Exporter:Export Format
Name of the output file that contains the exported data.
ProteomeDiscoverer:Spectrum Exporter:File name
ProteomeDiscoverer:Search Modifications Only For Identified Proteins
Standard high confidence XCorr parameter for charge = 1.
ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1
Standard high confidence XCorr parameter for charge = 2.
ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2
Standard high confidence XCorr parameter for charge = 3.
ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3
Standard high confidence XCorr parameter for charge >= 4.
ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4
Standard medium confidence XCorr parameter for charge = 1.
ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1
Standard medium confidence XCorr parameter for charge = 2.
ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2
Standard medium confidence XCorr parameter for charge = 3.
ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3
Standard medium confidence XCorr parameter for charge >= 4.
ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4
FT high confidence XCorr parameter for charge = 1.
ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
FT high confidence XCorr parameter for charge = 2.
ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
FT high confidence XCorr parameter for charge = 3.
ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
FT high confidence XCorr parameter for charge >= 4.
ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
FT medium confidence XCorr parameter for charge = 1.
ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
FT medium confidence XCorr parameter for charge = 2.
ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
FT medium confidence XCorr parameter for charge = 3.
ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
FT medium confidence XCorr parameter for charge >= 4.
ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter.
This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
ProteomeDiscoverer:1. Dynamic Modification
OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter.
ProteomeDiscoverer:2. Dynamic Modification
OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter.
ProteomeDiscoverer:3. Dynamic Modification
OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter.
ProteomeDiscoverer:4. Dynamic Modification
ProteomeDiscoverer:Static Modification for X
Minimal initial peptide probability to contribute to analysis.
ProteomeDiscoverer:Initial minimal peptide probability
Minimum adjusted peptide probability contributing to protein probability.
ProteomeDiscoverer:Minimal peptide probability
Minimum peptide weight contributing to protein probability.
ProteomeDiscoverer:Minimal peptide weight
Number of spectra from 1+ precursor ions.
ProteomeDiscoverer:Number of input1 spectra
Number of spectra from 2+ precursor ions.
ProteomeDiscoverer:Number of input2 spectra
Number of spectra from 3+ precursor ions.
ProteomeDiscoverer:Number of input3 spectra
Number of spectra from 4+ precursor ions.
ProteomeDiscoverer:Number of input4 spectra
Number of spectra from 5+ precursor ions.
ProteomeDiscoverer:Number of input5 spectra
Total number of predicted correct protein ids (sum of probabilities).
ProteomeDiscoverer:Number of predicted correct proteins
OBSOLETE Sample organism (used for annotation purposes).
Residues considered equivalent when comparing peptides.
ProteomeDiscoverer:Residue substitution list
This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead.
ProteomeDiscoverer:Source file extension
This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead.
ProteomeDiscoverer:WinCyg reference database
Determines if to use A ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of A Ions
Determines if to use B ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of B Ions
Determines if to use C ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of C Ions
Determines if to use D ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of D Ions
Determines if to use V ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of V Ions
Determines if to use W ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of W Ions
Determines if to use X ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of X Ions
Determines if to use Y ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of Y Ions
Determines if to use z ions for spectrum matching.
ProteomeDiscoverer:Mascot:Weight of Z Ions
Determines if to use precursor reevaluation.
ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation
Signal-to-Noise ratio below which peaks are removed (in FT mode only).
ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly
Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches.
ProteomeDiscoverer:Mascot:Please Do not Touch this
Phone number of the contact person or organization.
Fax number for the contact person or organization.
Toll-free phone number of the contact person or organization.
Significance threshold type used in Mascot reporting (either 'identity' or 'homology').
Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering').
List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'.
Waters LC-system ACQUITY UPLC H-Class Bio.
Waters LC-system ACQUITY UPLC Systems with 2D Technology.
Waters LC-system nanoACQUITY UPLC System with 1D Technology.
nanoACQUITY UPLC System with 1D Technology
Waters LC-system nanoACQUITY UPLC with HDX Technology.
Waters oa-ToF based MALDI Synapt G2 HDMS.
Waters oa-ToF based MALDI Synapt G2-S MS.
Waters (triple) quadrupole based Quattro micro GC.
NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences.
Waters Empower software for liquid chromatography and mass spectrometry acquisition.
Waters UNIFY software for liquid chromatography and mass spectrometry acquisition.
OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide.
This child of the former purgatory term ion mobility spectrometry was made obsolete.
travelling wave ion mobility mass spectrometer
LECO software for data acquisition and analysis.
Software for acquisition, processing and analysis of data for LECO instruments.
LECO high resolution time-of-flight GC mass spectrometer.
LECO high resolution time-of-flight LC mass spectrometer.
LECO GC time-of-flight mass spectrometer.
LECO bench-top GC time-of-flight mass spectrometer.
The data type of the value reported in a QuantLayer.
Attributes describing the details of an object relevant for reporting quantification workflows or values.
The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'.
The study variable is 'biological replicate'. This means, the run was generated from another individual or sample.
The experimental condition is 'case' in contrast to 'control'.
The experimental condition is 'control' in contrast to 'case'.
The experimental condition is 'disease' in contrast to 'healthy'.
The experimental condition is 'healthy' in contrast to 'disease'.
The experimental condition is given in the value of this term.
The experimental design followed a time series design. The time point of this run is given in the value of this term.
The experimental design followed a dilution series design. The concentration of this run is given in the value of this term.
The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free).
The raw file contains the run of two samples (e.g. SILAC, metabolic labelling).
The raw file contains the run of three samples (e.g. 3-plex SILAC).
The raw file contains the run of four samples (e.g. 4-plex iTraq).
The raw file contains the run of eight samples (e.g. 8-plex iTraq).
Attribute describing, how raw files build a raw file group.
The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given.
The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit.
Identifier for an SRM transition in an external document describing additional information about the transition.
Software from Nonlinear Dynamics for LC-MS label-free workflow.
Quantitation software comment or any customizations to the default setup of the software.
quantitation software comment or customizations
The overall workflow of this quantitation report.
SILAC workflow (heavy, light, and sometimes medium peak).
Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant).
Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range.
Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair).
Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens).
metabolic labeling 14N / 15N quantitation analysis
Maximum peak intensity of the LC-MS feature.
Real (intensity times area) volume of the LC-MS feature.
The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting.
OBSOLETE Area of MS1 peak (e.g. SILAC, 15N).
This term was made obsolete because it was a duplication of MS:1001844.
Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N).
Intensity of MS2 reporter ion (e.g. iTraq).
Simple ratio of two values (enumerator and denominator).
OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values.
This term was made obsolete because the concept MatchedFeature was dropped.
Protein quantification value calculated as sum of peptide values.
Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis).
Global datatype: p-value of ANOVA of group means (e.g. Progenesis).
Intensity (or area) of MS2 reporter ion (e.g. iTraq).
Normalized value of MS2 reporter ion (e.g. iTraq).
Area of the extracted ion chromatogram (e.g. of a transition in SRM).
Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM).
Protein quantification value calculated as mean of peptide ratios.
Terms used to describe types of quantification data processing.
Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting).
normalization to mean of sum of all proteins
Normalization of protein values to approach the same distribution.
Normalization of peptide values to approach the same distribution.
Automatic RT alignment of Progenesis software.
RT alignment of Progenesis software using automatic and manual vectors.
Normalization as performed by Progenesis LC-MS.
Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry).
Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0.
This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374).
The regular expression describing the sequence motif for a modification.
The a priori probability of a modification.
MALDI Solutions Microbial Identification
The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation.
The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum.
in-source collision-induced dissociation
Attributes of the quality of a transition that affect its selection as appropriate.
Variation of a set of signal measurements calculated as the standard deviation relative to the mean.
Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal.
Parameters string passed to a command-line interface software application, omitting the executable name.
Software for data analysis of peptides and proteins.
The data type normalised abundance for proteins produced by Progenesis LC-MS.
The data type normalised abundance for peptides produced by Progenesis LC-MS.
The data type raw abundance for proteins produced by Progenesis LC-MS.
The data type raw abundance for peptide produced by Progenesis LC-MS.
The data type confidence score produced by Progenesis LC-MS.
The data type peptide count produced by Progenesis LC-MS.
The data type feature intensity produced by Progenesis LC-MS.
The data type peptide counts (unique) produced by MaxQuant.
The data type peptide counts (all) produced by MaxQuant.
The data type peptide counts (razor+unique) produced by MaxQuant.
The data type sequence length produced by MaxQuant.
The data type PEP (posterior error probability) produced by MaxQuant.
The data type LFQ intensity produced by MaxQuant.
The data type feature intensity produced by MaxQuant.
The data type MS2 count produced by MaxQuant.
The emPAI value of protein abundance, produced from the emPAI algorithm.
The APEX value of protein abundance, produced from the APEX software.
The full width of a retention time window for a chromatographic peak.
Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source.
Thermo Scientific second generation Velos.
Thermo Scientific Orbitrap Elite, sometimes referred to as the LTQ Orbitrap Elite.
Thermo Scientific PinPoint SRM analysis software.
Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts.
Enzyme leukocyte elastase (EC 3.4.21.37).
Enzyme proline endopeptidase (EC 3.4.21.26).
Enzyme glutamyl endopeptidase (EC 3.4.21.19).
Main identifier of a ProteomeXchange dataset.
Version number of a ProteomeXchange accession number.
ProteomeXchange accession number version number
Free text attribute that can enrich the information about an entity.
Keyword present in a scientific publication.
Hash assigned by the Tranche resource to an individual file.
Hash assigned by the Tranche resource to a whole project.
URI that allows the access to one experiment in the PRIDE database.
URI that allows the access to one project in the PRIDE database.
Plate where the sample solution is spotted in a MALDI or similar instrument.
Whether the sprayer is fed or is loaded with sample once.
The sprayer is continuously fed with sample.
Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts.
LECO nominal mass resolution time-of-flight GCxGC mass spectrometer.
PEAKS Studio software for data analysis.
PEAKS Online software for high throughput data analysis.
PEAKS Node software for high throughput data analysis.
Bioinformatics Solutions Inc. Software for data processing and analysis.
Parameters used in the mass spectrometry acquisition.
Regular expression for leukocyte elastase.
Regular expression for proline endopeptidase.
Regular expression for glutamyl endopeptidase.
Algorithm used to score the match between a spectrum and a peptide ion.
peptide spectrum match scoring algorithm
Weighting factor for protein list compilation by ProteinExtractor.
Flag indicating a second round search with Mascot.
Flag indicating a second round search with Phenyx.
The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry.
OBSOLETE The ion drift time of an MS2 product ion.
This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476).
Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level.
phosphoRS score for PTM site location at the PSM-level.
Probability that the respective isoform is correct.
Estimate of the probability that the respective site is truly phosphorylated.
Version of the post-translational modification scoring algorithm.
The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value.
The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value.
The Phospho (STY) Probabilities from MaxQuant software.
The Phospho (STY) Score Diffs from MaxQuant software.
The P-site localization probability value from MaxQuant software.
MaxQuant:P-site localization probability
The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest).
A-score for PTM site location at the PSM-level.
H-Score for peptide phosphorylation site location.
Vacuum-drying MALDI sample preparation crystallization method.
Crushed-crystal MALDI sample preparation method.
crushed crystal MALDI sample preparation
Fast-evaporation MALDI sample preparation method.
fast evaporation MALDI sample preparation
Overlayer method combining features of the crushed-crystal method and the fast-evaporation method.
Sandwich MALDI sample preparation method.
Spin coating MALDI sample preparation method.
Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling.
quick and dirty MALDI sample preparation
Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'.
Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures.
The spectrum that will be baseline subtracted is divided into a number of segments.
The random noise is removed by using the undecimated wavelet transform.
It searches for known patterns in the measured spectrum.
sophisticated numerical annotation procedure
Normalization of areas below the curves.
A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID.
MS1 label-based raw feature quantitation.
MS1 label-based peptide level quantitation.
MS1 label-based protein level quantitation.
MS1 label-based proteingroup level quantitation.
A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys.
iRT retention time normalization standard
The type of the transitions, e.g. target or decoy.
A transition used to target a specific compound that may be in the sample.
A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows.
Quantitation analysis using an isobaric labelling workflow.
Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z.
Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score).
Collision energy at the start of the collision energy ramp.
Collision energy at the end of the collision energy ramp.
Spectral count peptide level quantitation.
Spectral count protein level quantitation.
Spectral count proteingroup level quantitation.
Label-free proteingroup level quantitation.
MS2 tag-based feature level quantitation.
MS2 tag-based peptide level quantitation.
MS2 tag-based protein level quantitation.
MS2 tag-based proteingroup level quantitation.
Nucleic acid base modification (substitution, insertion or deletion).
Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence.
Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence.
URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment.
URI that allows access to a PeptideAtlas dataset.
The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution.
The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution.
One of a set of authors associated with a publication or release.
A person who submits a dataset to a repository.
A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy".
Inlet properties that are associated with a value.
The temperature of the inlet of a mass spectrometer.
The temperature of the source of a mass spectrometer.
The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column.
ProteinProspector software for data acquisition and analysis.
The ProteinProspector result 'Expectation value'.
The original source path used for directory-based sources.
MS-GF software used to re-score the peptide-spectrum matches.
MS-GF+ software used to analyze the spectra.
As parameter for search engine: apply the modification only at the N-terminus of a protein.
As parameter for search engine: apply the modification only at the C-terminus of a protein.
Microsoft Excel (can be used for spectral counting).
The name of the UniProtKB/TrEMBL database.
OBSOLETE Decoy database from a TrEMBL protein sequence database.
Metabolic labelling: natural N (mainly 14N).
Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite.
Protein quantification value calculated as median of peptide ratios.
Metabolic labelling: heavy N (mainly 15N).
Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape.
Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed.
Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed.
P-value as result of one of the processing steps described. Specify in the description, which processing step it was.
The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'.
File format containing quantification results.
The mzQuantML format for quantification data from the PSI. File extension '.mzq'.
PAnalyzer software for getting protein evidence categories.
Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter.
This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
ProteomeDiscoverer:1. Static Modification
OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter.
ProteomeDiscoverer:2. Static Modification
ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column.
The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column.
Multidimensional chromatography modulation description.
Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition.
two-dimensional gas chromatography with fixed modulation time
Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time.
two-dimensional gas chromatography with discrete modulation time steps
Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition.
two-dimensional liquid chromatography with fixed modulation time
Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time.
two-dimensional liquid chromatography with discrete modulation time steps
XCorr threshold for storing peptides that do not belong to a protein.
ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated.
Delta Cn threshold for filtering out PSM's.
Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator.
Search engine input parameter that is shared by more than one search engine.
Search engine input parameters specific to Mascot.
Search engine input parameters specific to SEQUEST.
Search engine input parameters specific to Phenyx.
Search engine input parameters specific to ProteinExtractor.
Search engine input parameters specific to OMSSA.
Search engine input parameters specific to ProteinScape.
Search engine input parameters specific to ProteomeDiscoverer.
Software input parameter that is shared by more than one software.
Search engine input parameters specific to Scaffold.
Search engine input parameters specific to Percolator.
Indicates that a higher score is better.
Attribute describing a protein group list.
Attribute describing a peptide consensus list.
Attribute describing a peptide consensus.
Attribute describing a small molecule list.
Attribute describing a small molecule modification.
Dummy describing a spectral count feature.
X-Tracker generic tool for quantitative proteomics.
ProteoSuite software for the analysis of quantitative proteomics data.
OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools.
This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375).
The name of the UniProtKB knowledgebase.
Attribute describing an identification file.
Attribute describing a method file format.
Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment.
Attribute describing an identification file format.
Noise filter component of the TOPP software.
Removes noise from profile spectra by using a gaussian smoothing.
Removes noise from profile spectra by using a Savitzky-Golay smoothing.
Peak picker component of the TOPP software.
Finds mass spectrometric peaks in high-resoluted profile mass spectra.
Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra.
Spectra filter component of the TOPP software.
Applies a Bern et al normalization to peak spectra.
Applies a filter to peak spectra for marked peaks.
Retains the n largest peaks of a peak spectra.
Applies a TIC/maximal intensity normalization to peak spectra.
Filters putative unfragmented precursor ions from tandem spectra.
Applies a filter to peak spectra after intensity scaling according to rank.
Applies a filter to peak spectra after intensity scaling to the square root.
Applies a filter of peaks below a given threshold to peak spectra.
Applies a filter of the largest peaks in a sliding window over a peak spectrum.
Map aligner component of the TOPP software.
Corrects retention time distortions between maps based on common peptide identifications.
Corrects retention time distortions between maps using a pose clustering approach.
Corrects retention time distortions between maps by spectrum alignment.
Attribute describing the data type of the numerator of a ratio.
Attribute describing the data type of the denominator of a ratio.
The number of spectra identified for this protein in spectral counting.
Extracts spectra of an MS run file to several files in DTA format.
Merges several protein/peptide identification files into one file.
Converts identification engine file formats.
Merges spectra from an LC/MS map, either by precursor or by RT blocks.
Exports various XML formats to an mzTab file.
Annotates mass traces in centroided LC/MS maps.
Correct the precursor entries of tandem MS scans.
Performs precursor mz correction on centroided high resolution data.
Computes an additive series to quantify a peptide in a set of samples.
Decharges and merges different feature charge variants of the same chemical entity.
Quantifies signals at given positions in (raw or picked) LC/MS maps.
Feature finder component of the TOPP software.
Detects two-dimensional features in centroided LC-MS data.
Detects two-dimensional features in uncentroided LC-MS data.
Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm.
Detects two-dimensional features in centroided LC-MS data of metabolites.
Computes protein abundances from annotated feature/consensus maps.
Normalizes maps of one consensus XML file (after linking).
Applies retention time transformations to maps.
Feature linker component of the TOPP software.
Groups corresponding isotope-labeled features in a feature map.
Groups corresponding features from multiple maps.
Groups corresponding features from multiple maps using a quality threshold clustering approach.
Performs a peptide/protein identification with the CompNovo engine.
Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode.
Software adaptor to an external program in the TOPP software.
Identifies MS2 spectra using the external program Inspect.
Identifies MS2 spectra using the external program Mascot.
Identifies MS2 spectra using the online version of the external program Mascot.
Identifies MS2 spectra using the external program OMSSA.
Identifies MS2 spectra using the external program PepNovo.
Identifies MS2 spectra using the external program XTandem.
Identifies peptide MS2 spectra by spectral matching with a searchable spectral library.
Computes a consensus identification from peptide identifications of several identification engines.
Resolves ambiguous annotations of features with peptide identifications.
Filters results from protein or peptide identification engines based on different criteria.
Assigns protein/peptide identifications to feature or consensus features.
Estimates posterior error probabilities using a mixture model.
Calibrate Retention times of peptide hits to standards.
Refreshes the protein references for all peptide hits.
A tool for precursor ion selection based on identification results.
MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
OpenSwath component of the TOPP software.
Picks peaks and finds features in an SRM experiment.
Extract chromatograms (XIC) from a MS2 map file.
Generates decoys according to different models for a specific TraML.
Converts a featureXML to a mProphet tsv (tab separated values).
Generates a transformation file for retention time space into normalized space.
Infer proteins from a list of (high-confidence) peptides.
Estimates the false discovery rate on peptide and protein level using decoy searches.
Converts, filters, and processes mass spectrometry data in variety of formats.
Converts, filters, and processes identifications from shotgun proteomics experiments.
Filters and processes protein sequence databases.
Filters, processes, and displays mass spectrometry data in a variety of ways.
An interactive GUI application to view and filter mass spectrometry data in a variety of formats.
A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data.
The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation.
Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric.
A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum).
A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum).
A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum).
A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum).
A putative identified peptide issued from a decoy sequence database.
Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion.
Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion.
A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database.
Score in MRMaid to indicate the expected performance of the peptide in SRM.
Attribute associated with a SRM transition.
Probability of detecting precursor when parent protein is present.
Probability of detecting product ion when precursor ion is present.
Average value of product ion intensity in a collection of identified spectra.
Standard deviation of product ion intensity in a collection of identified spectra.
product ion intensity standard deviation
The number of times the specific product ion has been observed in a series of SRM experiments.
The number of times the specific precursor ion has been observed in a series of SRM experiments.
Calculated relaxed significance when performing a decoy search for high-confidence peptides.
ProteomeDiscoverer:Mascot:Significance Middle
Calculated relaxed significance when performing a decoy search for medium-confidence peptides.
ProteomeDiscoverer:Mascot:Significance High
The default FDR calculator as globally unique identifier (GUID).
ProteomeDiscoverer:Default FDR calculator
Flag indicating if low-resolution spectra are taken into consideration.
ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
Mass-to-charge ratio of a precursor ion selected for fragmentation.
A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores.
A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides.
A library of Java routines for manipulating mzIdentML files.
A converter for Tandem XML to mzIdentML.
A converter for CSV files (following OMSSA CSV style) to mzIdentML.
A generic and parameterizable protein inference algorithm for mzIdentML files.
A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files.
A routine for adding emPAI quantitative values to an mzIdentML file.
A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search.
A tool for converting mzIdentML files to CSV format.
A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file.
A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files.
Comet open-source sequence search engine developed at the University of Washington.
False-discovery rate threshold for peptide-spectrum matches.
Byonic search engine from Protein Metrics.
The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct.
The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct.
The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct.
The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism.
Best (most negative) log p-value of an individual PSM.
A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure.
Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid.
Gas chromatography (GC) is a separation technique in which the mobile phase is a gas.
Waters AutoSpec Premier magnetic sector instrument.
LECO nominal mass resolution time-of-flight GC mass spectrometer.
Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
Selected Reaction Monitoring feature level quantitation.
Selected Reaction Monitoring peptide level quantitation.
Selected Reaction Monitoring protein level quantitation.
Selected Reaction Monitoring proteingroup level quantitation.
A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology.
A software program that is a component of the Trans-Proteomic Pipeline.
A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format.
A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format.
A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format.
A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc.
A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc.
A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites.
Bruker Daltonics' SCION SQ: GC-single quadrupole.
Bruker Daltonics' SCION TQ: GC-triple quadrupole.
Bruker Daltonics' EVOQ Elite: LC-triple quadrupole.
Bruker Daltonics' EVOQ Qube: LC-triple quadrupole.
Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray.
Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion.
A detector using a fluorescent signal after excitation with light.
The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM.
The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein.
The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information.
Compression using MS-Numpress linear prediction compression.
MS-Numpress linear prediction compression
Compression using MS-Numpress positive integer compression.
MS-Numpress positive integer compression
Compression using MS-Numpress short logged float compression.
MS-Numpress short logged float compression
Indicates a consensus result from several search engine runs.
ProteomeDiscoverer:Amanda:high confidence threshold
ProteomeDiscoverer:Amanda:middle confidence threshold
Flag indicating automatic estimation of the workload level.
The Amanda score of the scoring function for a PSM.
ProteomeDiscoverer:max differential modifications
ProteomeDiscoverer:max equal modifications
ProteomeDiscoverer:max number neutral loss
Max number of same neutral losses of modifications.
ProteomeDiscoverer:max number neutral loss modifications
The maximum number of possible equal modifications per PSM.
ProteomeDiscoverer:max number of same modifs
Defines whether a simple deisotoping shall be performed.
Specifies the fragment ions and neutral losses that are calculated.
OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter.
ProteomeDiscoverer:3. Static Modification
OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter.
ProteomeDiscoverer:5. Dynamic Modification
The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group.
Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process.
Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML.
Java software designed to convert one of several proteomics identification results formats into PRIDE XML.
Amanda scoring system for PSM identification.
The probability based score of the Andromeda search engine.
Estimation of global false discovery rate of peptides with a post-translational modification.
Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project.
A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search.
A framework for differential analysis of mass spectrometry data.
Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers.
Attribute of a single peptide-spectrum match.
protein group-level identification attribute
Identification confidence metric for a peptide spectrum match.
Identification confidence metric for a protein group.
protein group-level identification statistic
Positive value range less than or equal to 1.
value greater than zero but less than or equal to one
Estimation of the global false discovery rate of peptide spectrum matches.
Estimation of the local false discovery rate of peptide spectrum matches.
Estimation of the p-value for peptide spectrum matches.
Estimation of the e-value for peptide spectrum matches.
Estimation of the q-value for peptide spectrum matches.
mzidLibrary FDRScore for peptide spectrum matches.
mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools.
Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum.
Search engine specific distinct peptide score.
search engine specific peptide sequence-level identification statistic
Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools.
distinct peptide-level combined FDRScore
Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs.
search engine specific score for proteins
Estimation of the local false discovery rate of proteins.
MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools.
MzidLibrary Combined FDRScore for proteins.
Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software.
Search engine specific protein group scores.
search engine specific score for protein groups
Estimation of the global false discovery rate of protein groups.
Estimation of the local false discovery rate of protein groups.
Estimation of the p-value for protein groups.
Estimation of the e-value for protein groups.
Estimation of the q-value for protein groups.
mzidLibrary FDRScore for protein groups.
mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools.
Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software.
Specifies the threshold value for relaxed scoring.
ProteomeDiscoverer:Relaxed Score Threshold
Specifies the threshold value for strict scoring.
ProteomeDiscoverer:Strict Score Threshold
Cut off score for storing peptides that do not belong to a protein.
ProteomeDiscoverer:Peptide Without Protein Cut Off Score
Estimation of the false localization rate for modification site assignment.
Software for automated LC-MALDI analysis and reporting.
SCiLS software for data acquisition and analysis.
PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis.
A compilation of search engine results in the PIA XML format.
A parameter set for a single PIA analysis.
Indicates whether the FDR score was calculated for the input file.
Indicates whether the combined FDR score was calculated for the PIA compilation.
Indicates whether PSM sets were created.
The number of top identifications per spectrum used for the FDR calculation, 0 means all.
The score given to a protein by any protein inference.
The used algorithm for the protein inference using PIA.
A filter used by PIA for the protein inference.
The used scoring method for the protein inference using PIA.
The used base score for the protein inference using PIA.
The method to determine the PSMs used for scoring by the protein inference.
A filter used for the report generation.
At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members.
Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence.
An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative.
The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file.
protein group-level result list attribute
The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file.
An identifier applied to protein groups to indicate that they are linked by shared peptides.
Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group.
Anubis software for selected reaction monitoring data.
The TraML format for transitions in SRM from the PSI. File extension '.TraML'.
Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM).
The background area for the quantified transition.
A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file.
Thermo Scientific Orbitrap Fusion with ETD.
URI that allows access to a PASSEL experiment.
Search engine input parameters specific to Paragon.
The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation.
The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation.
The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument.
The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search.
A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions.
The Paragon method setting that controls whether FDR analysis is conducted.
The Paragon method setting that controls whether quantitation analysis is conducted.
The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples.
The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity.
The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios.
Paragon: channel to use as denominator in ratios
Search engine specific metadata that are not user-controlled settings.
This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result.
Paragon: modified data dictionary or parameter translation
The time that a data processing action was started.
The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done.
The number of decoy sequences, if the concatenated target-decoy approach is used.
Information about the list of PSMs (SpectrumIdentificationList).
spectrum identification list result details
A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult.
A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult.
AIA Analytical Data Interchange file format for mass spectrometry data.
The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
AIA Analytical Data Interchange file format for chromatography data.
The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity.
The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity.
The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects.
Ion b-H3PO4: b ion with lost phosphoric acid.
Ion y-H3PO4: y ion with lost phosphoric acid.
No fixed modifications are included as a parameter for the search, and therefore they are not reported.
No variable modifications are included as a parameter for the search, and therefore they are not reported.
This term was obsoleted because it should be replaced by MS:1000336 with value H2O.
This term was obsoleted because it should be replaced by MS:1000336 with value NH3.
OBSOLETE Neutral loss of phosphoric acid.
This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4.
PeptideShaker is a software for the interpretation of proteomics identification results.
Estimation of the global false negative rate of protein groups.
Estimation of the global confidence of protein groups.
Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry).
peptide sequence-level global confidence
Estimation of the global false negative rate of peptide spectrum matches.
Estimation of the global confidence of peptide spectrum matches.
The probability based PeptideShaker PSM score.
The probability based PeptideShaker PSM confidence.
The probability based PeptideShaker peptide score.
The probability based PeptideShaker peptide confidence.
The probability based PeptideShaker protein group score.
The probability based PeptideShaker protein group confidence.
A collision-induced dissociation process that occurs in a trap-type collision cell.
trap-type collision-induced dissociation
The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine.
The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group.
ProteoAnnotator:non-canonical gene model score
The count of the number of peptide sequences mapped to non-canonical gene models only within the group.
ProteoAnnotator:count alternative peptides
Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated.
Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array.
Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum.
regular expression for a digital object identifier (DOI)
A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.
higher energy beam-type collision-induced dissociation
Estimated statistical threshold at PSM-level.
Estimated statistical threshold at peptide-level.
Estimated statistical threshold at protein-level.
Estimated statistical threshold at protein group-level.
protein group-level statistical threshold
Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
Details describing a special processing.
Modification localization scoring performed.
Consensus multiple search engine approach performed.
Group PSMs by distinct peptide sequence ignoring modifications.
Group PSMs by distinct peptide sequence with taking modifications into account.
group PSMs by sequence with modifications
Group PSMs by distinct peptide sequence with taking modifications and charge into account.
group PSMs by sequence with modifications and charge
This term was obsoleted because it was never intended to go in the CV.
A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file.
Indicating that no PSM threshold was used.
Indicating that no peptide-level threshold was used.
Flags a PSM that it is used for peptide-level scoring.
The order of modifications to be referenced elsewhere in the document.
regular expression for modification localization scoring
Mod position score: false localization rate.
modification rescoring:false localization rate
The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order.
Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order.
Crosslinked spectrum identification item.
The absolute abundance of protein in a cell.
States whether an internal peptide reference is used or not in absolute quantitation analysis.
States whether an internal protein reference is used or not in absolute quantitation analysis.
The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis.
The data type normalised abundance for protein groups produced by Progenesis LC-MS.
Progenesis:protein group normalised abundance
The data type raw abundance for protein groups produced by Progenesis LC-MS.
Peptide group identifier for peptide-level stats.
A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position.
Determine 1st static terminal post-translational modifications (PTMs).
ProteomeDiscoverer:1. Static Terminal Modification
Thermo Scientific PepFinder BioPharma analysis software.
Instrument specific scan properties that are associated with a value.
A data array of signal baseline values (the signal in the absence of analytes).
SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data.
Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger.
SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer.
D-Score for PTM site location at the PSM-level.
MD-Score for PTM site location at the PSM-level.
Localization confidence metric for a post translational modification (PTM).
PeptideShaker quality criteria for the confidence of PTM localizations.
PeptideShaker quality criteria for the confidence of PSM's.
PeptideShaker quality criteria for the confidence of peptide identifications.
PeptideShaker quality criteria for the confidence of protein identifications.
Target/Decoy based FDR estimation for crosslinking peptide-identifications.
A software package to convert Skyline report to mzQuantML.
A normalized spectral abundance factor (NSAF).
A distributed normalized spectral abundance factor (dNSAF).
distributed normalized spectral abundance factor
Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence.
PTM localization distinct peptide-level statistic
phosphoRS score for PTM site location at the peptide-level.
A-score for PTM site location at the peptide-level.
H-Score for peptide phosphorylation site location at the peptide-level.
D-Score for PTM site location at the peptide-level.
MD-Score for PTM site location at the peptide-level.
Threshold for Ascore PTM site location score.
Threshold for D-score PTM site location score.
Threshold for MD-score PTM site location score.
Threshold for H-score PTM site location score.
Threshold for DeBunker PTM site location score.
Threshold for Mascot PTM site assignment confidence.
Mascot:PTM site assignment confidence threshold
Threshold for MaxQuant:P-site localization probability.
MaxQuant:P-site localization probability threshold
Threshold for MaxQuant:Phospho (STY) Probabilities.
MaxQuant:Phospho (STY) Probabilities threshold
Threshold for phosphoRS site probability.
Number of spectra processed at once in a ProteomeDiscoverer search.
ProteomeDiscoverer:Number of Spectra Processed At Once
A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group.
A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group.
Estimated statistical threshold used for protein detection.
Estimated statistical threshold used for spectrum identification.
spectrum identification statistical threshold
A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc.
Tide open-source sequence search program developed at the University of Washington.
SCIEX TripleTOF 4600 time-of-flight mass spectrometer.
SCIEX TripleTOF 5600+ time-of-flight mass spectrometer.
Applied Biosystems/MDS SCIEX API 100 MS.
Applied Biosystems/MDS SCIEX API 100LC MS.
Applied Biosystems/MDS SCIEX API 165 MS.
Applied Biosystems/MDS SCIEX API 300 MS.
Applied Biosystems/MDS SCIEX API 350 MS.
Applied Biosystems/MDS SCIEX API 365 MS.
The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute.
Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches.
Spectral Hash key, an unique identifier for spectra.
Internal data and submission format of the PRIDE database.
Tabular result format for proteomics and metabolomics experiments.
Reagent used in labeled quantification methods.
The name of the sample labelled with the heavy ICAT label.
The name of the sample labelled with the light ICAT label.
The name of the sample labelled with the ICPL reagent 0.
The name of the sample labelled with the ICPL reagent 4.
The name of the sample labelled with the ICPL reagent 6.
The name of the sample labelled with the ICPL reagent 10.
Stable isotope labeling with amino acids in cell culture reagent.
The name of the sample labelled with the heavy SILAC label.
The name of the sample labelled with the medium SILAC label.
The name of the sample labelled with the light SILAC label.
Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling.
The name of the sample labelled with the TMT reagent 126.
The name of the sample labelled with the TMT reagent 127.
The name of the sample labelled with the TMT reagent 128.
The name of the sample labelled with the TMT reagent 129.
The name of the sample labelled with the TMT reagent 130.
The name of the sample labelled with the TMT reagent 131.
Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent.
The name of the sample labelled with the iTRAQ reagent 113.
The name of the sample labelled with the iTRAQ reagent 114.
The name of the sample labelled with the iTRAQ reagent 115.
The name of the sample labelled with the iTRAQ reagent 116.
The name of the sample labelled with the iTRAQ reagent 117.
The name of the sample labelled with the iTRAQ reagent 118.
The name of the sample labelled with the iTRAQ reagent 119.
The name of the sample labelled with the iTRAQ reagent 121.
Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy).
electron-transfer/higher-energy collision dissociation
Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
The name or number of the chromosome to which a given peptide has been mapped.
The strand (+ or -) to which the peptide has been mapped.
OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system.
This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome.
The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system.
The number of exons to which the peptide has been mapped.
A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length.
A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome.
The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference.
Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data.
Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formatted.
native spectrum identifier format, combined spectra
Thermo comma separated list of spectra that have been combined prior to searching or interpretation.
Thermo nativeID format, combined spectra
Waters comma separated list of spectra that have been combined prior to searching or interpretation.
Waters nativeID format, combined spectra
WIFF comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker/Agilent YEP nativeID format, combined spectra
Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker BAF nativeID format, combined spectra
Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker FID nativeID format, combined spectra
Comma separated list of spectra that have been combined prior to searching or interpretation.
multiple peak list nativeID format, combined spectra
single peak list nativeID format, combined spectra
scan number only nativeID format, combined spectra
spectrum identifier nativeID format, combined spectra
mzML unique identifier, combined spectra
Identification parameter for the search engine run.
Text-based format used by UniProtKB for sequence entries.
XML-based format used by UniProtKB for sequence entries.
Summed Morpheus score for protein groups.
Parent term for interaction scores derived from crosslinking.
interaction score derived from cross-linking
interaction score derived from crosslinking
regular expression for interaction scores derived from cross-linking
regular expression for interaction scores derived from crosslinking
Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114.
Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113.
Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N.
Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C.
No statistical threshold for accepting or rejecting that a modification position.
SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer.
This subsection describes terms which can describe details of crosslinking results.
Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments.
Estimation of the global false discovery rate of residue-pairs in crosslinking experiments.
A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation.
supplemental beam-type collision-induced dissociation
The dissociation of an ion after supplemental collisional excitation.
supplemental collision-induced dissociation
Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion.
OpenXQuest's combined score for a crosslink spectrum match.
OpenXQuest's cross-correlation of crosslinked ions subscore.
OpenXQuest's cross-correlation of unlinked ions subscore.
OpenXQuest's sum of matched peak intensity subscore.
OpenXQuest's weighted percent of total ion current subscore.
Attribute of an item in the result of mass spectrometry proteomics data analysis.
Statistic derived from a post-translational modification localization analysis.
Statistic for a single item derived from a post-translational modification localization analysis.
PTM localization single result statistic
Statistic for all items derived from a post-translational modification localization analysis.
Global false localization rate for all localizations in a dataset.
Local false localization rate for the bottom item in list of localizations sorted from most to least confident.
Attribute of an identification item in the result of mass spectrometry proteomics data analysis.
Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis.
Fragment ion corresponding to an isobaric label artifact.
Fragment ion that is an isotopic peak other than the monoisotopic peak. This is used in conjunction with another ion type, such as frag: y ion.
An attribute of the protein cluster concept as used in mzIdentML.
protein cluster identification attribute
General property of an entire result list.
General property of the list of all PSMs.
Statistic pertaining to the full list of all PSMs.
General property of all peptide sequences in the list.
peptide sequence-level result list attribute
Statistic pertaining to all peptide sequences in the list.
peptide sequence-level result list statistic
A statistical metric of an entire protein list.
Attribute of an entire list of protein groups.
protein group-level result list statistic
Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues.
A data type representing more than a single value.
A data type defining a list of values of a single type.
Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.
Representation of temperature versus time.
The component or dimension of an object being measured, for example the temperature of an instrument component over time.
Software for processing and exporting Waters MassLynx and waters_connect data.
PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra.
Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer.
Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer.
Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer.
Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer.
Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer.
Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer.
Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting.
The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting.
The data type of the value reported in a QuantLayer for a feature.
The data type of the value reported in a QuantLayer for a PSM.
The data type of the value reported in a QuantLayer for a peptide.
The data type of the value reported in a QuantLayer for a protein.
The data type of the value reported in a QuantLayer for a protein group.
protein group-level quantification datatype
Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location.
Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location.
A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array).
A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array).
A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array).
Compression using MS-Numpress linear prediction compression and zlib.
MS-Numpress linear prediction compression followed by zlib compression
Compression using MS-Numpress positive integer compression and zlib.
MS-Numpress positive integer compression followed by zlib compression
Compression using MS-Numpress short logged float compression and zlib.
MS-Numpress short logged float compression followed by zlib compression
Means that Mascot has integrated the search results of database and spectral library search into a single data set.
Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches.
MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum.
A combined MS2 (with fragment ions) and spectral library search.
combined ms-ms + spectral library search
Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow.
Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow.
Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow.
Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow.
Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow.
Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow.
Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow.
The name of the sample labelled with the TMT reagent 127N.
The name of the sample labelled with the TMT reagent 127C.
The name of the sample labelled with the TMT reagent 128N.
The name of the sample labelled with the TMT reagent 128C.
The name of the sample labelled with the TMT reagent 129N.
The name of the sample labelled with the TMT reagent 129C.
The name of the sample labelled with the TMT reagent 130N.
The name of the sample labelled with the TMT reagent 130C.
Deuterium isobaric amine reactive tag labeling reagent.
The name of the sample labelled with the DiART reagent 114.
The name of the sample labelled with the DiART reagent 115.
The name of the sample labelled with the DiART reagent 116.
The name of the sample labelled with the DiART reagent 117.
The name of the sample labelled with the DiART reagent 118.
The name of the sample labelled with the DiART reagent 119.
The name of the sample labelled with the DiLeu reagent 115.
The name of the sample labelled with the DiLeu reagent 116.
The name of the sample labelled with the DiLeu reagent 117.
The name of the sample labelled with the DiLeu reagent 118.
The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
Web search verification (2026-01-16) found no evidence that this Agilent model exists.
The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers.
The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers.
The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer.
The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer.
The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer.
Molecular entity having a net positive or negative electric charge.
Nonphysical characteristic attributed to an adduct ion.
Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator.
Isotope of the matrix molecule M of an adduct formation.
Regular expression for adduct ion formula
Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression.
An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm].
Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated.
Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array.
Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker TDF nativeID format, combined spectra
Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton.
Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M.
File format developed by the OpenMS team.
OpenMS intermediate identification format.
Feature intensity produced by XCMS findPeaks() from integrated peak intensity.
Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity.
Feature intensity produced by XCMS findPeaks() from maximum peak intensity.
Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate.
The scans of a run are acquired with polarities switching in a strictly alternating sequence (e.g., positive, negative, positive, negative), such that consecutive scans or scan cycles differ in polarity.
The Delta Score reported by Proteome Discoverer version 2.
Thermo Fisher Scientific LTQ Orbitrap Classic.
Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
mzMLb file format, mzML encapsulated within HDF5.
Conversion of a file format to Proteomics Standards Initiative mzMLb file format.
Data belonging to an external reference.
The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray.
The position in the external data where the array begins.
Describes how many fields an array contains.
Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam.
URI of one external file associated to the PRIDE experiment (maybe through a PX submission).
URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission).
URI associated to one PX submission in ProteomeCentral.
URI of one file labeled as 'Result', associated to one PX submission.
URI of one search engine output file associated to one PX submission.
URI of one of one search engine output file associated to one PX submission.
URI of one file labeled as 'Other', associated to one PX submission.
A dataset which does not have an associated published manuscript.
Dataset with no associated published manuscript
Dataset that has not been peer-reviewed by any means.
Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission.
Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission.
A dataset which has an associated manuscript pending for publication.
Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE.
URI of one gel image file associated to one PX submission.
All the raw files included in the original dataset (or group of original datasets) have been reanalysed.
A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed.
One dataset is a reanalysis of previously published data.
No post-translational-modifications are been included in the identified peptides of one dataset.
A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet.
Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet.
This means that the experimental information available has been improved, for instance precursor charges were added.
Experimental information has been refined since this experiment was originally made publicly available
One dataset is not a reanalysis of previously published data.
Bioconductor package mzR for reading and writing mass spectrometry data files.
Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.
Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication.
Thermo Scientific TSQ Altis Triple Quadrupole MS.
Thermo Scientific TSQ Quantis Triple Quadrupole MS.
Thermo Scientific TSQ 9000 Triple Quadrupole MS.
Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS.
Software for the analysis of small molecules.
Metabolomics analysis software for LC-MS data from Nonlinear Dynamics.
Metabolomics analysis software from Thermo Fisher Scientific.
Metabolite identification tool MyCompoundID.
Function used to calculate the study variable quantification value.
Function used to calculate the study variable quantification variation value.
The value reported in a small molecule quantification.
The normalised abundance produced by Progenesis QI LC-MS.
The confidence score produced by a small molecule analysis software.
The confidence score produced by Progenesis QI.
An attribute describing ion mobility searches.
Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided.
Unique chemical structure identifier for chemical compounds.
Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'.
compound identification confidence level
OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'.
This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.
Top-down mass spectral feature detection.
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.
proteoform-level identification attribute
Identification confidence metric for a proteoform.
proteoform-level identification statistic
Search engine specific proteoform scores.
search engine specific score for proteoforms
Estimation of the global false discovery rate of proteoforms.
Estimation of the local false discovery rate of proteoforms.
Estimated statistical threshold at proteoform-level.
Threshold for the global false discovery rate of proteoforms.
Threshold for the local false discovery rate of proteoforms.
Search engine input parameters specific to TopPIC.
Fixed modifications for TopPIC searching.
N-terminal forms of proteins allowed in TopPIC searching.
Error tolerance for precursor and fragment masses in PPM.
Maximum value of the mass shift (in Dalton) of an unexpected modification.
Minimum value of the mass shift (in Dalton) of an unexpected modification.
Maximum number of unexpected modifications in a proteoform spectrum match.
Spectrum-level cutoff type for filtering identified proteoform spectrum matches.
Spectrum-level cutoff value for filtering identified proteoform spectrum matches.
Proteoform-level cutoff type for filtering identified proteoform spectrum matches.
Proteoform-level cutoff value for filtering identified proteoform spectrum matches.
P-value and E-value estimation using generating function.
The text file containing the information of common PTMs.
Proteoform identification using TopFD feature file.
Search engine input parameters specific to TopMG.
Fixed modifications for TopMG searching.
N-terminal forms of proteins allowed in TopMG searching.
Maximum value of the mass shift (in Dalton).
Gap size in constructing proteoform graph.
Maximum number of variable PTMs in a proteoform graph gap.
TopMG:variable PTM number in proteoform graph gap
Protein filtering using ASF-DIAGONAL method.
Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry.
Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'.
hr-ms compound identification confidence level
A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'.
The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'.
The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'.
One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae.
An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms.
A molecular entity that differs only in isotopic composition (number of isotopic substitutions).
Lipid Data Analyzer software for lipid quantification.
The Lipid Data Analyzer native chrom format.
Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets.
Software for consensual cross-platform lipidomics.
An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.
Open-source software for automated phospholipid tandem mass spectrometry identification.
LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library.
A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms.
A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets.
An integrated software package for high-confidence lipid identification.
An-open source software for identifying lipids in LC-MS/MS-based lipidomics data.
Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1).
Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level.
Software tool for the quantitative analysis of mass spectrometric lipidome data.
Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers.
Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species.
The Proline software suite for mass spectrometry based proteomics.
PepNovo tool for de novo peptide sequencing.
pNovo tool for de novo peptide sequencing and identification using HCD spectra.
Novor real-time peptide de novo sequencing software tool.
Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes.
Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes.
ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra.
python-psims, a library for generating mzML and mzIdentML.
Thermo Scientific Orbitrap Exploris GC-MS.
Q Exactive Focus Hybrid Quadrupole-Orbitrap Mass Spectrometer.
Thermo Scientific Orbitrap Excedion Pro.
Posterior error probability of the best identified peptide of the Andromeda search engine.
Peak list file format of the Andromeda search engine.
Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD).
ProteomeXchange dataset identifier reanalysis number
Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS.
Shimadzu Scientific Instruments LCMS-8060 MS.
Shimadzu Scientific Instruments LCMS-8050 MS.
Shimadzu Scientific Instruments LCMS-8045 MS.
Shimadzu Scientific Instruments LCMS-8040 MS.
Shimadzu Scientific Instruments LCMS-2020.
Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array.
Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array.
Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array.
Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets.
Kernel mass spectral dot product scoring function.
i3-tms search engine and data-analysis software.
A database search-based peptide identification tool.
Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides.
Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins.
Fraction of peptide evidence attributable to a group of proteins.
General proteomics processing toolkit for shotgun proteomics.
Representation of chromatographic pressure versus time.
Representation of the chromatographic flow rate versus time.
Post-translational modification which is assumed to be present at each instance of a residue type.
Post-translational modification which may or may not be present at a residue type.
The OpenPepXL score for a crosslink spectrum match.
A named element that is an attribute in a proteomics standards file.
A named element that is an attribute in a mzIdentML file.
A named element that is an attribute in a mzML file.
Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS.
Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'.
The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program.
compound identification confidence code in MS-DIAL
Non-inherent characteristic attributed to a molecular entity.
Smallest constituent unit of ordinary matter that constitutes a chemical element.
Low molecular weight (< 900 daltons) organic compound that may regulate a biological process.
Small molecule that is the intermediate end product of metabolism.
Nucleotide containing ribose as its pentose component.
Monomer, or single unit, of DNA, or deoxyribonucleic acid.
Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid.
Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule.
Molecule composed of a chain of nucleotides.
Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages.
Number of amino acid residues in a peptide, commonly referred to as the peptide length.
Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not.
Process of mapping a peptide sequence to a protein sequence.
Nonphysical characteristic attributed to the result of peptide-to-protein mapping.
Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence.
Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules.
Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations.
Non-inherent characteristic attributed to a peptidoform.
Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'.
Inherent or measurable characteristic of a peptidoform ion.
Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents.
Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes.
Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species.
Physical measurable characteristic of an adduct ion.
Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run.
Inherent or measurable characteristic of a spectrum.
Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernible in the spectrum, which will be fewer than the number of data points.
Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks.
Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection.
Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0.
PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library.
Non-inherent characteristic attributed to spectrum aggregation.
Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.).
Spectrum that is not the result of some aggregation process.
Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates.
Spectrum that is considered the most representative from a pool of replicate spectra.
Number of replicate spectra available for use during the aggregation process.
Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm.
Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.).
Spectrum that originates from an analysis attempt of a single analyte species on an instrument.
Spectrum that originates from a compututational algorithm that attempts to predict spectra.
Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species.
Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features.
Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature.
Non-inherent characteristic attributed to an interpreted spectrum.
Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum.
Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum.
top 20 peak unassigned intensity fraction
Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML.
unidentified modification monoisotopic mass delta
Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors.
Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file).
File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument.
Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes.
Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope.
Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available.
supported by repository but incomplete data and/or metadata
Data array compression using mantissa bit truncation followed by zlib compression.
Data array compression using mantissa bit truncation, delta prediction and zlib compression.
truncation, delta prediction and zlib compression
Data array compression using mantissa bit truncation, linear prediction and zlib compression.
truncation, linear prediction and zlib compression
Settable parameter for a binary data compression event.
Number of extraneous mantissa bits truncated to improve subsequent compression.
Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues.
Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS.
Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS.
Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro.
The probability based MaxQuant protein group score.
Peptide probability from MaxQuant-DIA algorithm.
PSM evidence score from MaxQuant-DIA algorithm.
PSM evidence PEP probability from MaxQuant-DIA algorithm.
Term for a comment field within the NIST msp file format
Annotation format used for annotating individual spectrum ion peaks.
Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions.
Annotation format designed specifically for crosslinked peptide ion peaks.
cross-linked peptide ion annotation format
crosslinked peptide ion annotation format
Annotation format designed specifically for glycan ion peaks.
Annotation format designed specifically for lipid ion peaks.
PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data.
Identifying crosslinked peptides in complex protein mixtures
SIM-XL identification search engine score
Quantification of crosslinked peptides in complex protein mixtures
Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
The OpenMS ConsesusID tool posterior error probability
The score of the best PSM selected by the underlying identification tool
The OpenMS Target-decoy q-values at PSM level
The OpenMS Target-decoy q-values at peptide sequence level
The OpenMS Target-decoy q-values at protein level
A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework
Protein Posterior probability calculated by EPIFANY protein inference algorithm
The data type LFQ intensity produced by OpenMS.
The data type LFQ spectral count produced by OpenMS.
Bruker Daltonics' rapiflex: MALDI TOF/TOF.
Estimation of the Q-value for proteoforms.
Identification confidence metric for a isoform.
Search engine input parameters specific to ProSight.
Search engine input parameters specific to TDPortal.
If true, runs Subsequence Search mode in ProSight.
If true, runs Annotated Proteoform Search mode in ProSight.
ProSight:Run Annotated Proteoform Search mode
ProSight: Database search engine for top-down proteomics.
TDPortal: Database search engine for top-down proteomics.
Cross-platform software to convert Thermo RAW files to a number of open formats.
Python module that helps handling various proteomics data analysis tasks.
Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet.
PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet.
PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type.
PTMProphet normalized information content
PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type.
SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
Shimadzu Scientific Instruments GCMS-QP2010SE.
Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array.
Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array.
Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array.
deconvoluted inverse reduced ion mobility array
Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array.
deconvoluted ion mobility drift time array
Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum.
scanning quadrupole position lower bound m/z array
Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum.
scanning quadrupole position upper bound m/z array
Indicates an acquisition mode in which the instrument does not perform isolation or where the window spans the entire mass range of the precursor spectrum.
Proteomics Standards Initiative mzQC format for quality control data.
Grouping term for quality control data formats.
Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization.
The set of analyte identifiers that compose an interpretation of a spectrum.
QuaMeter IDFree software for QC metric calculation.
iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files.
Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum
The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte
A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools.
Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation
A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments
An entry in a spectral library representing a spectrum
An attribute that takes on a numeric value
The arithmetic mean value for this attribute
The standard deviation (exact value of population, or estimate from sample) of this attribute
The coefficient of variation of this attribute, i.e. standard deviation divided by the mean
The most appropriate summary value of the attribute, usually but not necessarily the mean
Combination of two or more dissociation methods that are known by a special term.
Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID).
electron-transfer/collision-induced dissociation
Waters oa-ToF based SELECT SERIES Cyclic IMS.
Version number of the [PSI] library format specification
Short identifier for the library for easy reference, preferably but not necessarily globally unique
A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library.
Extended free-text description of the library
Version number of the library, usually referring to a certain release of a continually updated library
URI or URL that uniquely identifies the library
A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching
A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence.
A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum.
A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform
A decoy spectrum that is a real spectrum of a naturally occurring peptidoform of an unrelated species that should not be found in the sample
URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)
Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work
Extended free-text description of the difference from the previous version
Version number of the software package used for library creation
Abstract term containing several different types of provenance information
A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington
Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible.
Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible
Source library URI which(at least) a subset of spectra were extracted from.
String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped
The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum.
The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum.
The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum.
A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library
A name to refer to a library attribute set
Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated.
Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated.
mass spectrometry acquisition method aspect
Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions.
Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once..
Mass spectrometer data acquisition method wherein a quadrupole mass analyzer transmits a sliding window of precursor ions for dissociation and spectrum acquisition within each acquisition cycle. This correlates precursor selection with product ion detection resulting in 'quadrupole transmission window' as an additional dimension in the resulting data. An example of such an approach is Waters SONAR.
dissociation of scanning quadrupole across a specified mass range
Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured.
Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement.
Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule.
Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run.
Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte.
Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC.
data independent acquisition from dissociation of sequential mass ranges
Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF.
data independent acquisition from dissociation of sequential mass ranges after ion mobility separation
Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF.
data independent acquisition from dissociation of full mass range after ion mobility separation
Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID.
data independent acquisition from dissociation of full mass range
Data independent mass spectrometer acquisition method wherein a quadrupole mass analyzer transmits a sliding window of precursor ions for dissociation and spectrum acquisition within each acquisition cycle. This correlates precursor selection with product ion detection resulting in 'quadrupole transmission window' as an additional dimension in the resulting data. An example of such an approach is Waters SONAR.
data independent acquisition from dissociation of scanning quadrupole across mass range
comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB).
An attribute that describes information about an entry in a spectral library
The ionization of analytes from a piece of paper by applying a solvent and voltage.
An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library.
A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library
A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library
A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores
A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots
A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks
The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton)
Accession number (e.g. in PeptideAtlas) of the peptide sequence
Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS.
Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons.
A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation.
Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation.
Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte.
The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence.
The number of spectra that pass the threshold to be considered identified with sufficient confidence.
Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer.
A universal software for data-independent acquisition (DIA) proteomics data processing
An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation.
For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution.
A link from one spectrum to another spectrum of interest
A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar.
A list of cross references to a related spectrum in the same library, in the form of the library spectrum key.
A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier
A free-text string describing the related spectrum and/or its relationship to this spectrum
A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion.
A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key.
A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier
A group of spectra that are spectrally similar to each other
A non-inherent characteristic of a spectrum cluster
An ordinal number uniquely identifying a spectrum cluster. It should start with 1.
A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library.
A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier.
A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type.
The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum.
A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'.
A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'.
A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1.
A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value
A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name
Value range for signed normalized score values.
A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte.
The frequency at which this peak is observed among replicate spectra of the same analyte.
A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte.
Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/.
Native format defined by frame=xsd:nonNegativeInteger.
Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation.
Bruker TSF nativeID format, combined spectra
The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte.
standard deviation of m/z values of peak among replicates
The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte.
coefficient of variation of intensity of peak among replicates
The standard deviation of the intensities of this peak among the replicate spectra of the same analyte.
standard deviation of intensity of peak among replicates
The number of unassigned peaks in the spectrum.
The intensity of the highest unassigned peak in the spectrum.
The number of unassigned peaks among the most intense 20 peaks in the spectrum.
number of unassigned peaks among top 20 peaks
Thermo Scientific TSQ Altis Plus Triple Quadrupole MS.
A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins.
Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum.
The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name'
number of replicates spectra used from source
A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum.
A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys.
A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers.
Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte.
Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence.
Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering.
A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone.
The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity.
The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space.
The number of peaks with closely matching m/z values that are common to two spectra.
The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi.
The Pearson's rho statistic between a pair of points representing two vectorized spectra.
The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature.
Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'.
Lipid shorthand identification confidence level
The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes.
Lipid shorthand identification confidence level 'Category'.
Lipid shorthand identification confidence - Category
Lipid shorthand identification confidence level 'Class'.
Lipid shorthand identification confidence - Class
Lipid shorthand identification confidence level 'Species'.
Lipid shorthand identification confidence - Species
Lipid shorthand identification confidence level 'Phosphate-position'.
Lipid shorthand identification confidence - Phosphate-position
Lipid shorthand identification confidence level 'Molecular species'.
Lipid shorthand identification confidence - Molecular species
Lipid shorthand identification confidence level 'sn-position'.
Lipid shorthand identification confidence - sn-position
Lipid shorthand identification confidence level 'DBE pos'.
Lipid shorthand identification confidence - DBE pos
Lipid shorthand identification confidence level 'Structure defined'.
Lipid shorthand identification confidence - Structure defined
The number of spectra in a spectrum cluster.
Summary statistics of an attribute among all spectra of a spectrum cluster.
Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not.
Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not.
Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum.
spectral dot product to aggregated spectrum
Lipid shorthand identification confidence level 'Full structure'.
Lipid shorthand identification confidence - Full structure
Lipid shorthand identification confidence level 'Complete structure'.
Lipid shorthand identification confidence - Complete structure
The number of protein groups that pass the threshold to be considered identified with sufficient confidence.
The number of proteoforms that pass the threshold to be considered identified with sufficient confidence.
Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink.
Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions.
noncovalently associated peptides search
Noncovalently associated peptides spectrum identification item.
Provides an identifier to encode identifications based on multiple spectra.
identification based on multiple spectra
regular expression for encoding identifications based on multiple spectra.
Parent term for PSM-level scores for identifications based on multiple spectra.
regular expression for PSM-level scores for identifications based on multiple spectra
PEP score for identifications based on multiple spectra.
posterior error probability from identification based on multiple spectra
Estimation of the global false discovery rate of crosslinked peptide spectrum matches.
Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides.
Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides.
Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI).
Protein-protein interaction passes threshold.
regular expression for whether interaction score derived from crosslinking passes threshold
States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences).
FDR applied separately to self crosslinks and protein heteromeric crosslinks
Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI).
This term indicates that a given protein modification is a derivative of a cleavable crosslinker.
The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’.
large-scale study of proteins and proteomes.
large-scale study of proteins and proteomes via the use of affinity reagents.
large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments.
study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins.
study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins.
study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins.
study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins.
study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins.
Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart.
The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score.
A p-value for the XCorr score, calculated using dynamic programming.
A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum.
The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks.
The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score.
The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure.
A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them.
The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value.
A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum.
The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution.
The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution.
The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution.
The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z.
reduction to summed singly charged peak list
The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer.
The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file.
specification document extension version
The versioning of an mzIdentML extension document.
Conversion of a file format to Open Chromatography Binary OCB file format.
ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH.
OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse.
Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer.
A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution.
asymmetric track lossless time-of-flight analyzer
Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer.
Waters Corporation RDa time-of-flight mass detector.
Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing.
The versioning of the crosslinking mzIdentML extension document.
mzIdentML crosslinking extension document version
Bioconductor package Spectra for mass spectrometry data representation and processing.
Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data.
Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries.
Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence.
Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots <name>:<mass>:<pairs with>.
A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses.
A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance.
RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF.
Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer.
The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file.
Software that creates or manipulates QC-related data.
An R package for reading, validating, and writing mzQC files.
A Java package for reading, validating, and writing mzQC files.
A Python package for reading, validating, and writing mzQC files.
IUPAC International Chemical Identifier.
MS1 recalibration using identified peptides as internal calibrants.
Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte.
Scout identification search engine score
Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer.
The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD).
Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology.
The Kojak score for an individual peptide sequence, similar to Comet:xcorr.
The Kojak expectation value for an individual peptide sequence.
The number of matched ions for an individual peptide sequence in a Kojak result.
The highest run of consecutive matched ions for an individual peptide sequence in a Kojak result.
The difference between the top Kojak score and the next best Kojak score for a PSM.
The rank of an individual peptide from the first pass of the Kojak scoring algorithm. Applies only to sequences in a crosslinked result.
The Kojak score for a crosslinked pair of peptide sequences, similar to Comet:xcorr.
The Kojak expectation value for a crosslinked pair of peptide sequences.
The number of matched ions for a crosslinked pair of peptide sequences in a Kojak result.
Orbitrap Exploris GC 240 Mass Spectrometer.
Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived.
selected fragment theoretical m/z observed intensity spectrum
Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data.
A software to identify cross-linked peptides from LC-MS/MS spectra.
A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data.
A software for interpreting protein quantification, interaction and post-translational modification data.
A computational platform for analyzing mass spectrometry-based proteomics data.
A software for LC-MS data management and analysis.
A tool for the analysis of chemically cross-linked proteins using mass spectrometry.
Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure.
Score difference to the second best identified peptide with a different amino acid sequence.
A serine protease that hydrolyzes peptide bonds at the C-terminus of threonine, alanine, serine, and valine. (EC:3.4.21.12)
Lowest ion mobility value observed in the ion mobility measurement array.
Highest ion mobility value observed in the ion mobility measurement array.
Representation of one or more spectra acquired across an ion mobility dimension.
An ion mobility frame where the ion mobility dimension is continuous.
An ion mobility frame where the ion mobility dimension is processed into discrete peaks of zero width.
Thermo Scientific Orbitrap Astral Zoom mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and an Astral analyzer.
A software for converting SCIEX wiff or wiff2 format to mzML.
Thermo Scientific ISQ 7000 Single Quadrupole GC-MS System.
DC potential at the start of the FAIMS voltage ramp.
DC potential at the end of the FAIMS voltage ramp.
SCIEX TripleTOF 6600+ triple quadrupole - time-of-flight mass spectrometer.
SCIEX Triple Quad 5500+ triple quadrupole mass spectrometer.
SCIEX Triple Quad 5500+ QTRAP Ready quadrupole - linear ion trap mass spectrometer.
Bruker APEX-Qe FT-ICR-MS mass spectrometer.
Bruker autoflex speed TOF/TOF MALDI TOF/TOF mass spectrometer.
Bruker esquire 3000 ion trap mass spectrometer.
Bruker maXis impact quadrupole time-of-flight mass spectrometer.
Bruker maXis impact HD quadrupole time-of-flight mass spectrometer.
Bruker maXis 3G quadrupole time-of-flight mass spectrometer.
Bruker solariX XR FT-ICR-MS mass spectrometer.
Bruker amaZon SL ion trap mass spectrometer.
Bruker EVOQ DART-TQ+ triple quadrupole mass spectrometer with Direct Analysis in Real Time (DART) ion source.
Bruker EVOQ LC-TQ triple quadrupole mass spectrometer.
Bruker EVOQ GC-TQ gas chromatograph - triple quadrupole mass spectrometer.
Bruker Toxtyper ion trap mass spectrometer.
Bruker impact II VIP quadrupole time-of-flight mass spectrometer.
Bruker ecTOF gas chromatograph - time-of-flight mass spectrometer.
Bruker autoflex maX MALDI TOF mass spectrometer.
Bruker rapifleX MALDI PharmaPulse MALDI TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability.
Bruker smartfleX MALDI TOF mass spectrometer.
Bruker neofleX MALDI TOF/TOF mass spectrometer.
Bruker MALDI Biotyper MALDI TOF mass spectrometer.
Bruker scimaX FT-ICR-MS mass spectrometer.
Bruker timsMetabo TIMS-Q-TOF mass spectrometer.
Bruker timsUltra AIP TIMS-Q-TOF mass spectrometer.
Bruker timsOmni TIMS-Q-TOF mass spectrometer.
Bruker timsTOF MALDI PharmaPulse MALDI TIMS-Q-TOF mass spectrometer with ultra-high-throughput screening (uHTS) capability.
Varian 4000 GC/MS gas chromatograph - ion trap mass spectrometer.
Varian 210-MS GC/MS Ion Trap gas chromatograph - ion trap mass spectrometer.
Shimadzu LCMS-8030 triple quadrupole mass spectrometer.
Shimadzu LCMS-8030 Plus triple quadrupole mass spectrometer.
Shimadzu GCMS-QP2010 Plus gas chromatograph - quadrupole mass spectrometer.
Shimadzu LCMS-8060NX triple quadrupole mass spectrometer.
Shimadzu GCMS-TQ8050NX gas chromatograph - triple quadrupole mass spectrometer.
Shimadzu GCMS-TQ8040NX gas chromatograph - triple quadrupole mass spectrometer.
Shimadzu GCMS-TQ8040 gas chromatograph - triple quadrupole mass spectrometer.
Shimadzu GCMS-QP5000 gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2020 gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2010 Ultra gas chromatograph - quadrupole mass spectrometer.
Thermo Fisher Scientific Velos Pro ion trap - mass spectrometer.
Thermo Fisher Scientific MALDI LTQ Orbitrap XL linear ion trap - orbitrap mass spectrometer.
Thermo Fisher Scientific MALDI LTQ Orbitrap Discovery linear ion trap - orbitrap mass spectrometer.
Thermo Fisher Scientific TSQ Quantum Access MAX triple quadrupole mass spectrometer.
Thermo Fisher Scientific LTQ Orbitrap Velos/ETD linear ion trap - orbitrap mass spectrometer.
Thermo Fisher Scientific ISQ LT gas chromatograph - quadrupole mass spectrometer.
Thermo Fisher Scientific ITQ ion trap mass spectrometer.
Thermo Fisher Scientific TSQ Quantum XLS gas chromatograph - triple quadrupole mass spectrometer.
Thermo Fisher Scientific TSQ 8000 gas chromatograph - triple quadrupole mass spectrometer.
Thermo Fisher Scientific DeltaPlus IRMS isotope ratio mass spectrometer.
Waters ACQUITY QDa quadrupole mass spectrometer.
Waters LCT Premier time-of-flight mass spectrometer.
Waters Quattro Premier XE triple quadrupole mass spectrometer.
Waters Synapt G1 HDMS quadrupole - ion mobility - time-of-flight mass spectrometer.
Waters Synapt G2-Si HDMS quadrupole - ion mobility - time-of-flight mass spectrometer.
Waters Synapt G1 quadrupole - ion mobility - time-of-flight mass spectrometer.
Waters Synapt G2 XS QTOF quadrupole - ion mobility - time-of-flight mass spectrometer.
Waters Xevo TQ Absolute triple quadrupole mass spectrometer.
Waters Xevo TQ Absolute XR triple quadrupole mass spectrometer.
Agilent 5973 MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5973N MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5975 MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5975B MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5975C inert XL MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5975C MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5975T MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5977 MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5977A MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5977B MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 5977C MSD gas chromatograph - quadrupole mass spectrometer.
Agilent 6230 Time-of-Flight LC/MS time-of-flight mass spectrometer.
Agilent 6410A Triple Quadrupole LC/MS triple quadrupole mass spectrometer.
Agilent 6445 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6456 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6470 Triple Quadrupole LC/MS triple quadrupole mass spectrometer.
Agilent 6490A Triple Quadrupole LC/MS triple quadrupole mass spectrometer.
Agilent 6495 Triple Quadrupole LC/MS triple quadrupole mass spectrometer.
Agilent 6520 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6530 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6543 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6545XT Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6546 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 6600 Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
Agilent 7000C Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer.
Agilent 7000D Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer.
Agilent 7010 Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer.
Agilent 7010B Triple Quadrupole GC/MS gas chromatograph - triple quadrupole mass spectrometer.
Agilent 7200 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer.
Agilent 7250 Q-TOF GC/MS gas chromatograph - quadrupole time-of-flight mass spectrometer.
Agilent CE-TOFMS capillary electrophoresis - time-of-flight mass spectrometer.
Agilent G3250AA Time-of-Flight LC/MS time-of-flight mass spectrometer.
Agilent Revident Q-TOF LC/MS quadrupole time-of-flight mass spectrometer.
LECO Pegasus BT 4D GCxGC - time-of-flight mass spectrometer.
LECO Pegasus HT gas chromatograph - time-of-flight mass spectrometer.
LECO Pegasus IV time-of-flight mass spectrometer.
Ionicon Analytik PTR-TOF 8000 proton-transfer-reaction - time-of-flight mass spectrometer.
JEOL AccuTOF GCv gas chromatograph - time-of-flight mass spectrometer.
IONTOF TOF.SIMS 5 time-of-flight secondary ion mass spectrometer.
PerkinElmer TurboMass GC/MS gas chromatograph - quadrupole mass spectrometer.
Thermo Finnigan ThermoQuest Voyager gas chromatograph - quadrupole mass spectrometer.
Shimadzu AXIMA-LNR MALDI TOF mass spectrometer.
Shimadzu AXIMA-TOF² MALDI TOF/TOF mass spectrometer.
Shimadzu AXIMA Resonance MALDI TOF mass spectrometerwith Ion Trap for MSn.
Shimadzu MALDI-8020 benchtop MALDI TOF mass spectrometer.
Shimadzu MALDI-8030 benchtop MALDI TOF mass spectrometer.
Shimadzu MALDI-8020 EasyCare benchtop MALDI TOF mass spectrometer.
Shimadzu MALDI-8030 EasyCare benchtop MALDI TOF mass spectrometer.
Shimadzu LCMS-2010 quadrupole mass spectrometer.
Shimadzu LCMS-2050 quadrupole mass spectrometer.
Shimadzu LCMS-8045RX triple quadrupole mass spectrometer.
Shimadzu LCMS-8050RX triple quadrupole mass spectrometer.
Shimadzu LCMS-8060RX triple quadrupole mass spectrometer.
Shimadzu LCMS-8065XE triple quadrupole mass spectrometer.
Shimadzu LCMS-9050 quadrupole time-of-flight mass spectrometer.
Shimadzu GCMS-QP5050A gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2010S gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2010 gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2020NX gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-QP2050 gas chromatograph - quadrupole mass spectrometer.
Shimadzu GCMS-TQ 8030 gas chromatograph - triple quadrupole mass spectrometer.
Shimadzu GCMS-TQ 8050 gas chromatograph - triple quadrupole mass spectrometer.
Associating of product ions with the precursor from which they are derived, by comparing retention time and, where appropriate, ion mobility peaks.
The methods, technology and chemistry by which a hyphenated separation system effects the separation of compounds.
OBSOLETE. The methods, technology and chemistry by which a liquid chromatography system effects the separation of compounds.
Ion-exchange chromatography is a technique used to separate molecules based on their surface charge. The process relies on the reversible electrostatic interaction between charged molecules in a sample and an oppositely charged stationary phase, typically a resin in a column.
Size-exclusion chromatography (SEC), also known as gel filtration chromatography (GFC) or gel permeation chromatography (GPC), is a chromatographic technique that separates molecules based on their size or, more precisely, their hydrodynamic volume in solution. This method is primarily used for the separation of large molecules like proteins and polymers.
Affinity chromatography (AC) is a highly selective separation technique used to purify specific biomolecules from complex mixtures, leveraging their unique biological or chemical interactions with an immobilized ligand.
Reversed-phase (RP) chromatography is a technique used to separate compounds based primarily on their hydrophobicity.
Normal-phase (NP) chromatography is a technique used to separate compounds based primarily on their polarity.
Hydrophilic Interaction Liquid Chromatography (HILIC) is a chromatographic technique for the separation of polar and hydrophilic compounds. HILIC employs a polar stationary phase that absorbs water from the mobile phase to form a hydrophilic layer that retains polar analytes.
hydrophilic interaction liquid chromatography
Chiral separation in liquid chromatography is the process of resolving enantiomers.
Mixed-mode separation in liquid chromatography uses stationary phases that combine multiple types of interactions to retain and separate compounds.
Hydrophobic Interaction Chromatography (HIC) is a type of chromatography used to separate biomolecules, typically proteins, based on their differences in surface hydrophobicity.
An on-line coupled system to effect separation of compounds prior to detection with a spectrometric or other detection technology.
Liquid chromatography (LC) is an analytical technique used to separate a mixture into its individual components for identification, quantification, and purification. The separation is based on the differential interactions of the sample compounds with a liquid mobile phase and a solid stationary phase.
A system for High-Performance Liquid Chromatography (HPLC), a widely used analytical chemistry technique for separating, identifying, and quantifying individual components in a liquid mixture.
high-performance liquid chromatography system
A system for Ultra-Performance Liquid Chromatography (UPLC), a trademark of the Waters Corporation and is largely synonymous with ultra-high performance liquid chromatography.
ultra-performance liquid chromatography system
A system for Ultra-High Performance Liquid Chromatography (UHPLC), an advanced form of high-performance liquid chromatography designed to achieve significantly faster, higher-resolution, and more sensitive separations. It is primarily achieved by innovations in particle chemistry and systemation capable of handling ultra-high pressures.
ultra-high performance liquid chromatography system
A system for Fast Protein Liquid Chromatography (FPLC), a versatile and widely used medium-pressure chromatography technique primarily employed for the separation and purification of biomolecules, especially proteins. It operates under low to moderate pressures, making it suitable for labile proteins and other large biomolecules that might be denatured by the high pressures and organic solvents often used in high-performance liquid chromatography.
fast protein liquid chromatography system
A system for Three-dimensional liquid chromatography (3D-LC), an advanced separation technique that combines three distinct liquid chromatography (LC) methods to achieve significantly enhanced separation power for complex mixtures, particularly in fields like proteomics.
three-dimensional liquid chromatography system
A system for on-line planar chomatography.
A system for on-line Thin Layer Chromatography (TLC), based upon a widely used, simple, and cost-effective analytical technique for separating and identifying components in a mixture.
A system for on-line High-Performance Thin Layer Chromatography (HPTLC), an advanced and refined version of traditional Thin Layer Chromatography (TLC), designed to offer significantly improved performance in terms of resolution, sensitivity, and reproducibility. It utilizes finer and more uniformly sized stationary phase particles, leading to more efficient separations and more accurate quantitative analysis.
high-performance thin layer chromatography system
A system for two-dimensional liquid chromatography (2D-LC), also often referred to as LC-LC or LC×LC, an advanced analytical technique that combines two different liquid chromatography methods in series to achieve enhanced separation of complex mixtures. It offers significantly higher resolving power and peak capacity compared to conventional one-dimensional liquid chromatography (1D-LC).
two-dimensional liquid chromatography system
Nano-flow LC at a typical flow rate in the nL/min range (e.g., 50-1000 nL/min) with a typical column internal diameter of ≤ 0.1 mm, commonly used for high sensitivity, low sample volume applications.
Capillary-flow LC at a typical flow rate of 2-10 µL/min with a typical column internal diameter of 0.3-0.5 mm, commonly used for high sensitivity applications.
capillary-flow liquid chromatography system
Micro-flow, or microbore, LC at a typical flow rate of 10-50 µL/min with a typical column internal diameter of 1.0 mm, commonly used for increased sensitivity application and lower solvent consumption.
Analytical scale LC at a typical flow rate between 0.2- 3 mL/min with a typical column internal diameter of 2.1-4.6 mm, commonly used in typical LC methodology.
Semi-preparative LC at a typical flow rate between 5-50 mL/min with a typical column internal diameter of 10 mm, commonly used for the small scale purification and isolation of compounds.
semi-preparative liquid chromatography system
Preparative LC at a typical flow rate of > 50 mL/min with a typical column internal diameter of > 20 mm, commonly used for the large scale purification and isolation of bulk quantities of target compounds.
preparative liquid chromatography system
Liquid chromatography system model name not including the vendor's name.
Waters Corporation liquid chromatography system model.
Waters liquid chromatography system model
Bruker software for untargeted metabolomics and lipidomics data analysis.
Bruker software for target screening and quantitation.
Proteomics Standards Initiatve mzPeak file format.
InstaNovo is a deep learning based tool using a Transformer architecture for de novo peptide sequencing.
InstaNovo+ is a deep learning based tool using a Diffusion architecture for de novo peptide sequencing.
Advion Interchim Scientific liquid chromatography system model.
Advion liquid chromatography system model
Agilent Technologies liquid chromatography system model.
Agilent liquid chromatography system model
Agilent 1200 Series Rapid Resolution RRLC system.
Agilent 1290 Infinity 2D-LC 2D-LC UHPLC system.
Agilent 1290 Infinity II 2D-LC 2D-LC UHPLC system.
Agilent 1260 Infinity III Prime UHPLC system.
The theoretical monoisotopic mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's monoisotopic mass plus the mass of a proton).
The theoretical average mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's average mass plus the average mass of a hydrogen ion).
The theoretical neutral monoisotopic mass of the molecule (e.g. the peptide sequence and its modifications), not including its charge carrier.
The theoretical neutral average mass of the molecule (e.g. the peptide sequence and its modifications), not including its charge carrier.
Beckman Coulter, Inc. liquid chromatography system model
Beckman Coulter liquid chromatography system model
Beckman Coulter System Gold HPLC system.
Bruker Corporation liquid chromatography system model
Bruker liquid chromatography system model
Bruker Michrom BioResources Paradigm MS4 2D-LC HPLC system.
Bruker Michrom Advance nanoflow UHPLC system.
SCIEX liquid chromatography system model
SCIEX Eksigent ekspert nanoLC 400 HPLC system.
SCIEX Eksigent ekspert nanoLC 425 HPLC system.
SCIEX Eksigent ekspret ultraLC 100 UHPLC system.
SCIEX Eksigent ekspert ultraLC 100-XL UHPLC system.
SCIEX Eksigent ekspert ultraLC 110 UHPLC system.
SCIEX Eksigent NanoLC-Ultra 2D 2D-LC UHPLC system.
Hitachi, Ltd. liquid chromatography system model
Hitachi liquid chromatography system model
JASCO, Inc. liquid chromatography system model
JASCO liquid chromatography system model
Shimadzu Corporation liquid chromatography system model
Shimadzu liquid chromatography system model
Shimadzu Prominence UFLC XR UHPLC system.
Shimadzu LC-2040C 3D Nexera-i HPLC system.
Shimadzu Prominence Plus LC-30 HPLC system.
Thermo Scientific liquid chromatography system model.
Thermo Dionex Integrion HPIC ion chromatography system.
Thermo Dionex Integrion RFIC ion chromatography system.
Thermo Dionex UltiMate 3000 RSLC UHPLC system.
Thermo Dionex UltiMate 3000 RSLCnano UHPLC system.
Thermo Dionex UltiMate 3000 UHPLC system.
Thermo Dionex UltiMate 3000 XRS UHPLC system.
Thermo Dionex ICS-5000+ ion chromatography system.
Thermo Proxeon EASY-nLC II UHPLC system.
Thermo Cohesive Technologies TX2 HPLC system.
Thermo Flux Instruments Rheos Allegro UHPLC pump.
Thermo Flux Instruments Rheos 2000 Micro HPLC pump.
Thermo Flux Instruments Rheos 2200 Micro HPLC pump.
Waters ACQUITY UPLC H-Class PLUS UPLC system.
Waters ACQUITY UPLC I-Class PLUS UPLC system.
Waters ACQUITY UPLC M-Class UPLC system.
Waters Alliance 2695 Separations Module HPLC system.
Fast gas chromatography (fast GC, FGC) employs short, narrow-bore capillary columns, high carrier gas velocity, and rapid temperature programming to achieve high-efficiency separations in a fraction of standard GC run times.
Packed column gas chromatography uses stainless steel or glass tubes (typically 2–4 mm ID, 1–6 m length) filled with particulate packing material coated with stationary phase, enabling the separation of larger sample volumes but typically providing lower efficiency and broader peaks than capillary GC.
Capillary column gas chromatography uses narrow-bore fused silica columns (typically 0.1–0.5 mm ID, 5–100 m length) coated with a thin internal stationary phase, enabling high-efficiency, high-resolution separations of volatile analytes.
High-resolution gas chromatography (HRGC) utilizes narrow-bore capillary columns and optimized parameters to achieve exceptional separation efficiency and peak capacity for complex, volatile mixtures.
Pyrolysis-gas chromatography (Py-GC) thermally decomposes complex samples into smaller volatile fragments, which are separated using GC.
Gas-liquid chromatography (GLC) employs an inert gaseous mobile phase and a liquid stationary phase immobilized on a solid support, separating volatile analytes by differential partitioning in the column.
Non-polar stationary phase gas-liquid chromatography employs phases like polydimethylsiloxane (PDMS), where separation is based on analyte volatility and dispersion interactions, optimally retaining non-polar compounds.
non-polar stationary phase gas-liquid chromatography
Mid-polar stationary phase gas-liquid chromatography employs phases such as polysiloxanes, providing balanced separation through both dispersion and dipole interactions for analytes of intermediate polarity.
mid-polar stationary phase gas-liquid chromatography
Polar stationary phase gas-liquid chromatography uses stationary phases such as polyethylene glycol, maximizing retention and selectivity for polar analytes via dipole–dipole and hydrogen bonding interactions.
polar stationary phase gas-liquid chromatography
Chiral stationary phase gas-liquid chromatography uses a stationary phase with bonded chiral selectors, enabling enantiomeric separation by stereoselective interactions.
chiral stationary phase gas-liquid chromatography
Gas-solid chromatography (GSC) separates volatile analytes by adsorption onto a solid stationary phase, with elution governed by analyte–surface interactions and adsorption.
Molecular sieve stationary phase gas–solid chromatography separates volatile analytes by differential adsorption onto a porous, crystalline aluminosilicate solid phase, enabling selective separation of permanent gases and small hydrocarbons.
molecular sieve stationary phase gas-solid chromatography
Porous polymer stationary phase gas-solid chromatography employs solid adsorbents like porous polystyrene-divinylbenzene, enabling volatile analyte separation by selective physical adsorption based on molecular size and polarity.
porous polymer stationary phase gas-solid chromatography
Activated carbon stationary phase gas-solid chromatography utilizes activated carbon’s high surface area to selectively adsorb and resolve volatile non-polar organics and permanent gases via surface interactions and physical adsorption.
activated carbon stationary phase gas-solid chromatography
Inorganic oxides stationary phase gas-solid chromatography employs solid adsorbents such as silica or alumina, enabling separation of permanent gases and low-boiling organics by surface adsorption interactions.
inorganic oxides stationary phase gas-solid chromatography
Graphitized carbon stationary phase gas-solid chromatography utilizes non-porous or porous graphitized carbon, enabling strong planar and π-electron interactions for selective adsorption and separation of aromatic and polar analytes.
graphitized carbon stationary phase gas-solid chromatography
A gas chromatography (GC) system comprises an injector, temperature-controlled column with stationary phase, carrier gas supply, oven, and detector, enabling separation of volatile analytes.
A two-dimensional gas chromatography system (GC×GC) uses orthogonal column sets connected by a modulator, providing enhanced separation of complex mixtures via sequential, independent mechanisms in primary and secondary columns.
two-dimensional gas chromatography system
Gas chromatography system model name not including the vendor's name.
Agilent Technologies gas chromatography system model.
A gas chromatography mass spectrometry system (GC–MS) integrates a gas chromatograph for volatile analyte separation with a mass spectrometer for ionization and detection, enabling sensitive qualitative or quantitative analysis.
gas chromatography mass spectrometry system
Gas chromatography mass spectrometry system model name not including the vendor's name.
gas chromatography mass spectrometry system model
Shimadzu Corporation gas chromatography mass spectrometry system model.
Shimadzu gas chromatography mass spectrometry system model
A system to effect separation of compounds.
Hewlett Packard gas chromatography system model.
Hewlett Packard 5890 Series gas chromatograph.
Hewlett Packard 5890 Series II gas chromatograph.
PerkinElmer gas chromatography system model.
PerkinElmer AutoSystem XL GC gas chromatograph.
Shimadzu Corporation gas chromatography system model.
Shimadzu gas chromatography system model
Shimadzu GC-2010 Plus gas chromatograph.
Thermo Scientific gas chromatography system model.
Thermo TRACE GC Ultra gas chromatograph.
Instruments classified based on their architecture with respect to mass analyzers.
A triple quadrupole mass spectrometer (TQMS; QqQ) is a tandem mass spectrometry (MS/MS) system that employs three linear quadrupoles in series to achieve highly selective and sensitive targeted quantification of specific compounds. The first quadrupole (Q1) may select a precursor ion, the second (Q2) induces fragmentation via collision-induced dissociation (CID), and the third (Q3) monitors specific product ions, typically through Multiple Reaction Monitoring (MRM).
A quadrupole time-of-flight (Q-TOF) mass spectrometer is a hybrid instrument that combines a quadrupole mass filter with a time-of-flight (TOF) mass analyzer to provide both highly accurate mass measurements and fragmentation data. The quadrupole may be used to select a specific precursor ion which is then fragmented, and the resulting product ions are measured by the TOF analyzer, providing high resolution and mass accuracy for structural elucidation and quantification.
An ion trap time-of-flight (IT-TOF) mass spectrometer is a hybrid instrument that uses an ion trap to accumulate, store, and often fragment ions, which are then periodically injected into a time-of-flight (TOF) mass analyzer for high-resolution mass analysis. This combination allows for sensitive MSn experiments (multiple stages of mass spectrometry) within the ion trap for structural elucidation and provides high mass accuracy and resolution via the TOF component.
A triple quadrupole linear ion trap (QqLIT) mass spectrometer is a hybrid instrument that can operate as a conventional triple quadrupole for high-sensitivity quantification (e.g., in Multiple Reaction Monitoring mode) or as a linear ion trap for qualitative analysis, such as MSn experiments and structural elucidation. The final quadrupole (Q3) of the system can be rapidly switched between functioning as a mass-resolving filter and a high-capacity linear ion trap, allowing for both precise quantification and comprehensive structural information to be acquired in a single analytical run.
A quadrupole Fourier-transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer is a hybrid instrument that uses an initial quadrupole for ion guiding or mass filtering before the ions are introduced into a Penning trap, where the mass analysis occurs. Once in the Penning trap, the ions' mass-to-charge ratios (m/z) are determined with ultra-high resolution and mass accuracy by measuring their unique cyclotron frequencies in a strong magnetic field and converting the resulting image current signal into a mass spectrum via a Fourier transform.
quadrupole fourier transform ion cyclotron resonance
A quadrupole ion mobility time-of-flight (Q-IMS-TOF) mass spectrometer is a hybrid instrument that adds an ion mobility spectrometry (IMS) cell between the quadrupole and the time-of-flight (TOF) analyzer, providing an additional dimension of separation based on ion size, shape, and charge in a buffer gas. This configuration allows for the separation of isobars and isomers that have the same mass-to-charge ratio (m/z) but different three-dimensional structures, which significantly enhances analytical confidence for complex samples such as in proteomics, environmental analysis, and drug screening.
A hybrid instrument that combines an ion trap for ion storage and fragmentation with an Orbitrap mass analyzer for high-resolution, accurate-mass (HRAM) detection.
A quadrupole Orbitrap mass spectrometer is a hybrid instrument that uses a quadrupole mass filter for precursor ion selection, a collision cell for fragmentation, followed by an Orbitrap mass analyzer which determines the precise mass-to-charge ratios of ions with high resolution and mass accuracy via Fourier transform.
A mass spectrometer that integrates a quadrupole mass filter, a linear ion trap, and an Orbitrap mass analyzer to provide precursor ion selection, multiple-stage fragmentation (MSn), and ultra-high resolution mass analysis.
A instrument that integrates a quadrupole mass filter, an Orbitrap mass analyzer, and the ASTRAL analyzer for high performance in ion selection, high-resolution analysis, and high-speed, high-sensitivity MS2 measurements.
The scans of a run include both positive and negative polarity acquisitions in a pattern that is not strictly alternating, such as discrete blocks of each polarity, irregular switching sequences, or other non-alternating arrangements.
Secondary electrospray ionization (SESI) is an atmospheric pressure ionization (API) technique that uses a primary nano-electrospray plume of solvent ions to ionize neutral gaseous molecules in the gas phase via efficient proton transfer reactions. Operating at atmospheric pressure, SESI allows for the sensitive and real-time detection of volatile organic compounds (VOCs) and vapors with minimal sample preparation, making it ideal for applications like breath analysis and environmental monitoring.
The ion polarity configuration used during data acquisition of a sample run.
Zstandard compression, a fast, modern, general purpose lossless compression algorithm.
Byte shuffle transform followed by Zstandard compression.
Dictionary encoding followed by Zstandard compression using a sorted dictionary with separately byte-shuffled values and indices.
Compression using MS-Numpress linear prediction compression and Zstandard .
MS-Numpress linear prediction compression followed by zstd compression
Compression using MS-Numpress positive integer compression and Zstandard.
MS-Numpress positive integer compression followed by zstd compression
Compression using MS-Numpress short logged float compression and Zstandard.
MS-Numpress short logged float compression followed by zstd compression
Electrophoretic separation is a technique in which charged analytes are separated by differential migration in an applied electric field.
Capillary electrophoresis (CE) is an electrophoretic separation technique performed in narrow-bore capillaries, in which analytes migrate through an electrolyte solution under the influence of an electric field and separate according to their electrophoretic mobility.
Electrochromatography is a liquid chromatography technique in which the mobile phase is driven through a stationary phase by electroosmotic flow generated by an applied electric field, combining electrophoretic migration with chromatographic retention.
Ion-pair reversed-phase chromatography is a reversed-phase chromatography technique in which an ion-pairing reagent is added to the mobile phase to enable retention and separation of charged or ionizable analytes on a nonpolar stationary phase.
Supercritical fluid chromatography (SFC) is a separation technique in which the mobile phase is a fluid above and relatively close to its critical temperature and pressure.
Thermo Scientific TSQ Certis Triple Quadrupole MS.
OpenMS TOPP tool to assemble metabolite features from singleton mass traces.
Apply an algorithm to remove excess zero intensity value data points from a spectrum. Data may be retained for interperatbility such as retaining only zeros that flank non-zero intensity value data points from a profile spectrum..
A zero intensity point trimming algorithm that interpolates the m/z coordinate values from the local data or an estimated model.
zero intensity point trimming interpolation
A strategy for mass spectrometry-based analysis that defines whether analytes are predetermined or discovered during acquisition.
An analytical approach in which comprehensive detection of all measurable analytes is attempted without prior specification of target compounds.
An analytical approach in which a predefined set of analytes is measured, typically enabling quantitative determination.
An analytical approach combining targeted monitoring of predefined analytes with simultaneous untargeted data acquisition.
Parallel Reaction Monitoring (PRM) utilizes high-resolution, accurate-mass mass spectrometry, typically a quadrupole orbitrap or quadrupole time-of-flight instrument, to isolate specific precursor ions and detect all resulting product ions in parallel. Unlike Selected Reaction Monitoring (SRM), which filters for pre-selected transitions, PRM acquires full MS/MS spectra for each target, thereby eliminating the need for transition optimization and providing high specificity through high-resolution interference rejection.
Agilent Technologies gas chromatography mass spectrometry system model.
Agilent gas chromatography mass spectrometry system model
Comprehensive two-dimensional gas chromatography (GCxGC) is a multidimensional separation technique that utilizes two columns with different stationary phases connected by a modulator, which traps, focuses and reinjects fractions from the first column to the second. This approach leads to a 2D chromatogram offering higher peak capacity and separation power.
PSI Quality Control controlled vocabulary term.
Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations.
The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix.
Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value).
Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable).
Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value).
The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns.
A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable).
The actual structure of the matrix is defined in the mzQC specification document.
QC metric based on identification results.
QC metric not based on identification results.
QC metric based on quantification results.
QC metric calculated from a single run (e.g. one .raw file).
QC metric calculated from multiple runs (e.g. multiple .raw files).
QC metric calculated from a single spectrum.
QC metric calculated from multiple spectra.
QC metric related to an extracted ion chromatogram.
QC metric related to the mass spectrometry acquisition.
QC metric related to events in the ion source.
QC metric related to the sample preparation.
QC metric related to measurements of the ambient environment, such as the laboratory.
Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time.
The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied.
Factors like temperature, airflow, or instrument calibration can cause mass shifts.
The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000178 for the MS1 equivalent.
The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000179 for the MS1 equivalent.
The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra.
The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides.
The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra.
The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides. Issues such as contamination on the MS front-end and fragmentation efficiency can lead to poor MS signals. Contamination would decrease both MS1 and MS2 S/N, while poor fragmentation efficiency affects MS2 signal but leaves MS1 signal unchanged.
The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030).
Poor fragmentation efficiency or precursor fragmentation intensity thresholds affect MS2 signal but leave MS1 signal unchanged.
The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC.
This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly.
The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3.
OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3.
The retention time duration of the chromatography in seconds.
Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument.
OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run.
OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type.
OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation.
OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3
The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant.
OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples.
An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode.
MS1 peak density distribution - quantiles
The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode.
MS2 peak density distribution - quantiles
The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher.
the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2.
The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states.
MS2 unknown and likely precursor charges fractions
Fastest frequency for MS level 1 collection
Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
Fastest frequency for MS level 2 collection
The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds.
The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well.
Upper and lower limit of m/z precursor values at which MSn spectra are recorded.
The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode.
Upper and lower limit of retention time at which spectra are recorded.
An unusual low range may indicate incomplete sampling and/or a premature or failed LC run.
The number of chromatograms recorded for the run.
Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum.
A QC metric based on a QC sample of known content.
A QC metric based on a QC sample of known and high complexity content.
A QC metric based on a QC sample of known and low complexity content.
A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design.
Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'
A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design).
Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK'
Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected.
Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected.
QC terms associated but not directly metrics themselves.
Data from the first principal component of a PCA.
Data from the second principal component of a PCA.
Data from the third principal component of a PCA.
Data from the fourth principal component of a PCA.
Data from the fifth principal component of a PCA.
Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels.
Used to supply alternative labels for plotting figures.
Used to supply batch label information with any string value.
Used to supply injection sequence information with consecutive whole numbers.
A table with the PCA results of MaxQuant's protein group raw intensities.
principal component analysis of MaxQuant's protein group raw intensities
A table with the PCA results of MaxQuant's protein group lfq intensities.
principal component analysis of MaxQuant's protein group lfq intensities
A table with the PCA results of identified MS1 feature areas.
identified MS1 feature area principal component analysis result
A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas.
unidentified MS1 feature area principal component analysis result
A table with the PCA results of identified MS1 feature areas after batch-correction.
batch-corrected identified MS1 feature area principal component analysis result
The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
slowest frequency for MS level 1 collection
The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
slowest frequency for MS level 2 collection
The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans.
An unusual high count of signal jumps or falls may indicate ESI stability issues.
The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans.
Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).
An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).
Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).
The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run.
number of detected quantification data points
The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
number of identified quantification data points
Tabular representation of the total ion current detected in each of a series of mass spectra.
Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition.
Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)
Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content.
MS1 frequency in equal parts of subsequent RT
Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)
MS2 frequency in equal parts of subsequent RT
From the distribution of peak densities in MS1, the mean
The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
From the distribution of peak densities in MS1, the sigma value
From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold
MS1 peak density distribution low outliers
From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold
MS1 peak density distribution high outliers
From the distribution of peak densities in MS2, the mean
The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings.
From the distribution of peak densities in MS2, the sigma value
From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold
MS2 peak density distribution low outliers
From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold
MS2 peak density distribution high outliers
From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3.
The intensity distribution of the precursors informs about the dynamic range of the acquisition.
From the distribution of MS2 precursor intensities, the mean
MS2 precursor intensity distribution mean
From the distribution of MS2 precursor intensities, the sigma value
MS2 precursor intensity distribution sigma
From the distribution of precursor intensities, the list of outliers below a in-file defined threshold
MS2 precursor intensity distribution low outliers
From the distribution of precursor intensities, the list of outliers above a in-file defined threshold
MS2 precursor intensity distribution high outliers
From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3
The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors.
From the distribution of signal-to-noise ratio in MS1, the mean
The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
From the distribution of signal-to-noise ratio in MS1, the sigma value
From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold
From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold
From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3
A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
From the distribution of signal-to-noise ratio in MS2, the mean
From the distribution of signal-to-noise ratio in MS2, the sigma value
From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold
From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold
From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3
Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
From the distribution of ion injection times (MS:1000927) for MS1, the mean
From the distribution of ion injection times (MS:1000927) for MS1, the sigma value
From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold
From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold
From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3
From the distribution of ion injection times (MS:1000927) for MS2, the mean
From the distribution of ion injection times (MS:1000927) for MS2, the sigma value
From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold
From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold
The definition of the outlier criteria applied.
Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5.
Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5.
Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5.
Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3.
Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used.
A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc.
The goodness of fit statistic between observed retention times and iRT calibrated retention times.
MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.
Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
The m/z distribution informs about the dynamic range of the acquisition.
MS2 precursor median m/z of identified quantification data points
The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
interquartile RT period for identified quantification data points
The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
Higher rates may indicate a more efficient sampling and identification.
rate of the interquartile RT period for identified quantification data points
The area under the total ion chromatogram.
The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content.
The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content.
Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
The metric informs about the dynamic range of the acquisition.
extent of identified MS2 precursor intensity
Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
The metric informs about the dynamic range of the acquisition along the chromatographic separation.
median of TIC values in the RT range in which the middle half of quantification data points are identified
Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
median of TIC values in the shortest RT range in which half of the quantification data points are identified
Minimum and maximum MS2 precursor intensity recorded.
From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
The metric informs about the dynamic range of the acquisition in relation to identifiability.
identified MS2 precursor intensity distribution
From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
unidentified MS2 precursor intensity distribution
From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
identified MS2 precursor intensity distribution mean
From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
unidentified MS2 precursor intensity distribution mean
From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
identified MS2 precursor intensity distribution sigma
From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
unidentified MS2 precursor intensity distribution sigma
The ratio of 1+ over 2+ MS2 precursor charge count of all spectra.
High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization.
ratio of 1+ over 2+ of all MS2 known precursor charges
The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability.
ratio of 1+ over 2+ of identified MS2 known precursor charges
The ratio of 3+ over 2+ MS2 precursor charge count of all spectra.
Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides.
ratio of 3+ over 2+ of all MS2 known precursor charges
The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability.
ratio of 3+ over 2+ of identified MS2 known precursor charges
The ratio of 4+ over 2+ MS2 precursor charge count of all spectra.
ratio of 4+ over 2+ of all MS2 known precursor charges
The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
ratio of 4+ over 2+ of identified MS2 known precursor charges
Mean MS2 precursor charge in all spectra
Higher charges may indicate inefficient ionization or e.g. preference for longer peptides.
Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability.
mean MS2 precursor charge in identified spectra
Median MS2 precursor charge in all spectra
Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides.
Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability.
median MS2 precursor charge in identified spectra
The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database).
"High values may indicate a sample handling issue, and/or insufficient sample concentration."
The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher.
OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration.
The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation.
obsolete identified MS2 quarter RT fraction
The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode.
The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode.
The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode.
The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode.
The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode.
The metric informs about the dynamic range of the acquisition along the chromatographic separation. This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant.
The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode.
The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.
DIAMetric is a Data-Independent Acquisition Quality Metric Generator.
The amount of time elapsed since the start of the data acquisition until the implied quantile of all MS1 TIC has been accumulated. The number of values in the tuple implies the quantile mode.
The amount of time elapsed since the start of the data acquisition until the implied quantile of all MS2 TIC has been accumulated. The number of values in the tuple implies the quantile mode.
The median time between consecutive MS1 scans across the full run.
The median time between consecutive measurements of the same DIA isolation window across the full run.
The number of distinct DIA isolation windows (i.e. sharing the same low m/z boundary, high m/z boundary, and ion mobility parameters).
The minimum and maximum m/z width of the DIA isolation windows, defined as the subtraction between the high m/z boundary and the low m/z boundary. For fixed-window DIA methods, the same value is reported twice.
The minimum and maximum number of times any specific DIA isolation window is measured via MS/MS. In case all isolation windows are sampled the same number of times, this value is reported twice.
The minimum and maximum retention time in which at least half of the TIC for any given DIA isolation window compared to the full TIC in this isolation window has been collected.
The minimum and maximum TIC collected in any given DIA isolation window.
"Because isolation windows measure different m/z regions, the TIC for their MS/MS signals may vary considerably from each other."
For each DIA isolation window, we compute the median number of peaks per MS/MS measurement. This metric reports the lowest and highest peak count medians among the isolation windows.
Outlier score for MS runs based on the median Euclidean distance for each run to every other run after robust PCA transformation of the QC metrics for all runs.
Outlier score for MS runs based on the local outlier probabilities (LoOP) algorithm applied to QC metrics from all runs.
The maximum base peak intensity (MS:1000505) of all spectra in a single run.
The maximum base peak intensity (MS:1000505) of all spectra in a single run in the given retention time ranges. The time windows are specified by the 2nd column defining the start time in seconds and the 3rd column defining the duration in seconds. To define a range from a starting time until the run's end, -1 may be used for the duration with 0 for the start.
base peak intensity maxima per time ranges
The maximum total ion current (MS:1000285) of all spectra in a single run.
The maximum total ion current (MS:1000285) of all spectra in a single run in the given retention time ranges. The time windows are specified by the 2nd column defining the start time in seconds and the 3rd column defining the duration in seconds. To define a range from a starting time until the run's end, -1 may be used for the duration with 0 for the start.
total ion current maxima per time ranges
The quantiles of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied. E.g. one value triplet represents the quartiles Q1, Q2, Q3.
The fraction of all data points detected for quantification purposes within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher.
detected quantification data points charges fractions
The fraction of all data points detected and identified for quantification purposes within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher.
identified quantification data points charges fractions
The fraction of filtered peptide spectrum matches (PSMs) within the run for each specified charge state. The fractions [0,1] are given in the 'fraction' column, corresponding charges in the 'charge state' column. The highest charge state is to be interpreted as that charge state or higher. The numbers here are recorded after any filtering for PSM level quality (e.g. FDR filtering).
peptide spectrum matches charges fractions
The vacuum pump pressure of a run, defined by the retention times and respectively applied pressures. The values are similar to the ones saved in MS:1000821, but using a tabular representation.
Tabular representation of the total ion current (TIC) of the MS1 spectra. It is a tabular representation of the total ion current detected in each of a series of mass spectra versus time (similar to the MS:1000235, but a mzQC valid table), using only the MS1 spectra.
Tabular representation of the total ion current (TIC) of the MS2 spectra. It is a tabular representation of the total ion current detected in each of a series of mass spectra versus time (similar to the MS:1000235, but a mzQC valid table), using only the MS2 spectra.
Observed and expected characteristics for spiked in or reference peptides. The expected peptides are encoded by proforma peptidoform sequence (MS:1003169). The 'predicted retention time' should be interpreted as the expected retention time of a reference measurement.
characteristics of spike in and reference peptide
The number of accessions in identified protein ambiguity groups that have been identified. This is the number of accessions in the groups, which were counted in 'MS:1002404 ! count of identified proteins', which hence must be greater or equal to this number.
number of all identified accessions in all ambiguity groups
The fraction of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective fraction of such peptides identified in the 'fraction' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher.
A practiced and regimented skill or series of actions.
A method of analyzing or representing statistical data; a procedure for calculating a statistic.
An organizational header for concepts representing mostly abstract entities.
A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
Terms used to indicate units of time or other terms associated with time.
The period of time during which something continues.
A numeral or string of numerals expressing value, quantity, or identification.
The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
A term that helps define and render a concept unique.
An active process; excludes processes and mechanisms which fulfill biological functions.
One of the axes representing the projection of variance resulting from principal component analysis.
Span a region or interval of distance, space or time.
An observation in a data set that is numerically distant from the rest of the data.
PSI Extended FASTA Format controlled vocabulary term.
CV term that may appear in a PEFF file header section.
CV term that may appear in a description line of a PEFF file individual sequence entry.
PEFF keyword for the sequence database name.
PEFF keyword for the sequence database prefix.
PEFF keyword for the sequence database short description.
PEFF keyword for the specifying whether the sequence database is a decoy database.
PEFF keyword for the source of the database file.
PEFF keyword for the database version (release date) according to database provider.
OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider.
PEFF keyword for the sumber of sequence entries in the database.
PEFF keyword for the description of the conversion from original format to this current one.
PEFF keyword for the molecular type of the sequences.
PEFF keyword for database specific keywords not included in the current controlled vocabulary.
PEFF keyword for the specific values for a custom key.
PEFF keyword for the short description of the PEFF file.
PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms.
PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location.
PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation.
DbUniqueId shall not be used in the PEFF 1.0 serialization as it is redundant with the primary identifier following the >
PEFF keyword for the NCBI taxonomy identifier.
PEFF keyword for the taxonomy name (latin or common name).
PEFF keyword for the Protein Evidence; A UniProtKB code 1-5.
PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains.
OBSOLETE Sequence variation (substitution, insertion, deletion).
This term was made obsolete in favor of VariantSimple and VariantComplex.
PEFF keyword for the modified residue with PSI-MOD identifier.
PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier.
PEFF keyword for the Alternative Accession Code.
PEFF keyword for the sequence status. Complete or Fragment.
PEFF keyword for the entry associated comment.
PEFF keyword for the entry associated keyword(s).
PEFF keyword for the Gene Ontology code.
PEFF keyword for the cross-reference to an external resource.
Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed.
Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein.
Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle.
PEFF keyword for the sequence conflict; a UniProtKB term.
PEFF keyword for the Sequence checksum in crc64.
PEFF keyword for the sequence range of a domain.
PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term.
PEFF keyword for the modified residue with UniMod identifier.
PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term.
PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon.
PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers.
PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications.
PEFF keyword describing the type of processing event being described.
PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary.
Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide.
N-terminal methionine residue of a protein that can be co-translationally cleaved.
PSequence shall not be used in the PEFF 1.0 serialization as it is redundant with the sequence line
regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
regular expression for PEFF molecular sequence type
regular expression for PEFF sequence status
A unit of measurement is a standardized quantity of a physical quality.
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is equal to one thousandth of a second or 10^[-3] s.
A time unit which is equal to 60 seconds.
A unit which is one of a particular measure to which all measures of that type can be related.
A unit which is a standard measure of the amount of a 2-dimensional flat surface.
A density unit which is a standard measure of the mass of a substance in a given volume.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A unit which is a standard measure of the number of repetitive actions in a particular time.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A unit which is a standard measure of the force applied to a given area.
A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2].
A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc).
An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force.
A unit which is a standard measure of the figure or space formed by the junction of two lines or planes.
A unit which is a standard measure of the angle formed by two straight lines in the same plane.
A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s.
A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance.
A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6].
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A unit which is a standard measure of the influence exerted by some mass.
A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad.
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
A dimensionless ratio unit which denotes numbers as fractions of 100.
A dimensionless unit which denotes a simple count of things.
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field.
An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy.
An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state.
A mass unit which is equal to one thousand daltons.
A unit which is a standard measure of the strength of a magnetic field.
A magnetic flux density unit which is equal to one weber per square meter.
A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J.
The electric field strength is a unit which is a measure of the potential difference between two points some distance apart.
The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart.
A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light.
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long.