I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd:string, ...)
Fragmentation method used for dissociation or fragmentation
Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
A sample that has not been labelled or modified
The date on which data creation began [NCI]
Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam
Root node for terms relating to the description of a protocol as ordered steps, in relation to the PRIDE.xml element ExperimentCollection/Experiment/Protocol/ProtocolSteps/StepDescription
Protocol step description additional parameter
Root node for terms relating to the description of a ModificationItem (post translational modification or artifactual modification) in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/ModificationItem/additional/cvParam
Root node for terms relating to the description of a PeptideItem in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/additional/cvParam
Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam
Root node for terms relating to the description of a Gel in relation to the PRIDE.xml element ExperimentCollection/Experiment/TwoDimensionalIdentification/Gel/additional/cvParam
Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam
Version number / identifier for search engine.
Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam
Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen. NOTE: A request has been made to have this concept added to MeSH. Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept.
To make something soluble or more soluble, especially in water, by the action of a detergent or other agent.
The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components.
Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)
To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time.
The removal of a region of a gel which contains protein(s) of interest.
The fragmentation of proteins into peptides through the use of an enzyme such as trypsin.
The transfer of an alkyl group from one molecule to another.
This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
Valid values for cvLabel entries referencing external database / CV / ontology.
Valid value for the cvLabel entry referencing PubMed.
Valid value for the cvLabel entry referencing PRIDE
Valid value for the cvLabel entry referencing GO.
Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)
Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy.
Valid value for the cvLabel entry referencing the PSI ontology
Valid value for the cvLabel entry referencing UNIMOD
Valid value for the cvLabel entry referencing RESID.
Valid value for the cvLabel entry referencing ISBN
Any technique which separates differentiated structures from the cell.
This CV term should be used in association with a value that is a free-text description of the experiment.
Final correlation score rank and preliminary score rank.
m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom).
the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide.
Any sequence reported before the start of the peptide.
Any sequence reported after the end of the peptide sequence.
Score as defined for the Mascot search algorithm.
Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project.
A qualifier is mandatory when using this term. The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only.
Indistinguishable alternative protein accession
The probability score for this peptide assignment to be correct, as calculated by PeptideProphet.
The probability score for this protein identification to be correct, as calculated by ProteinProphet.
The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime.
The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double.
The width of the referenced gel image in pixels. Mandatory value of type xsd:int.
The height of the referenced gel image in pixels. Mandatory value of type xsd:int.
Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification.
The intensity of the spot on the gel. Mandatory value of type xsd:double.
The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double.
The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double.
A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment.
The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included.
The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching.
The name of the sample labelled with iTRAQ reagent 114.
The name of the sample labelled with iTRAQ reagent 115.
The name of the sample labelled with iTRAQ reagent 116.
The name of the sample labelled with iTRAQ reagent 117.
The intensity of the sample labelled with iTRAQ reagent 114.
The intensity of the sample labelled with iTRAQ reagent 115.
The intensity of the sample labelled with iTRAQ reagent 116.
The intensity of the sample labelled with iTRAQ reagent 117.
A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures.
Two Dimensional Polyacrylamide Gel Electrophoresis
Electrophoresis using an gel which has a pH gradient along its length.
A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE.
Sodium dodecyl sulfate polyacrylamide gel electrophoresis
The lowest pH of an immobilised pH gradient gel.
The highest pH of an immobilised pH gradient gel.
The length in centimeters of an immobilised pH gradient gel.
This value associated with this CV term should always be in centimeters.
Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters.
This CV term should be used in association with a value that is a free-text description of the first dimension details
Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis.
This CV term should be used in association with a value that is a free-text description of the second dimension details
A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values.
The method by which the normalized value for spot volume is derived from the individual gel spot volume values.
The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146).
A substance that prevents coagulation; that is, it stops blood from clotting.
Date of last mapping of given identifier to current UniProt accession number.
Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found' .
Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession' .
Error message: Error with queried database.
Error message: Unable to match given identifier.
Error message: One or more peptide sequences did not match query sequence.
Error message: No mapping to proteins from defined taxon.
Sucessful completion of operation message.
A Score based on the hypergeometric model.
The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together.
The Sum of all penalties for the peptide assignment.
The reading direction on the DNA is 5' to 3'.
The reading direction on the DNA 3' to 5'.
type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g. .
range of acceptable fragment masses accepted by instrument.
number of missed cleavage sites taken into account.
Sucessful mapping without supporting evidence from peptides.
PICR tool has allocated the accession number.
Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist.
Detailed information about a genomic locus identified by whole genome searches.
Start position of the nucleic acid sequence on the chromosome
Stop position of the nucleic acid sequence on the chromosome
Value of average of all individual peptide identifications for this protein.
Value of average of all individual peptide scores.
The software which was used to generate the PRIDE XML file.
The X!Tandem hyperscore for the peptide.
The Spectrum Mill score for the peptide.
A protocol step to select for a particular type of peptides.
Search parameter that allows users to find query results from old data.
B ion type with a neutral loss of an ammonia group.
B ion type with a neutral loss of a water molecule.
Y ion type with the neutral loss of a molecule water.
Y ion type with the neutral loss of an ammonia group.
Ion resulting from in-source fragmentation.
Fragment ion that could not be assigned to a predicted fragment ion mass.
Fragment ion that was matched to another, co-eluting peptide precursor.
A general term for any stable isotope method.
The precise amino acid that has been modified.
Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates.
Ratio of peptide pair the sequence/sample is the numerator in the ratio.
This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample.
Expect value as defined for the Mascot search algorithm.
Probability that the top match is correct.
ProteomExchange accession number of the project where the PRIDE experiment is included.
ProteomExchange project accession number
Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included.
Original format of the file containing MS data.
m/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge.
average iTRAQ ratio sample over control.
Average spectrum iTRAQ ratio (=geometric mean) for the peptide.
Average spectrum iTRAQ ratio (=geometric mean) for the protein.
Number of quantified spectra contributing to the protein iTRAQ ratio.
protein iTRAQ ratio number of contributing spectra
Geometric sample standard deviation of the protein iTRAQ ratio.
X ion type with the neutral loss of a molecule water.
X ion type with the neutral loss of an ammonia group.
Z ion type with the neutral loss of a molecule water.
Z ion type with the neutral loss of an ammonia group.
A ion type with the neutral loss of a molecule water.
A ion type with the neutral loss of an ammonia group.
C ion type with the neutral loss of a molecule water.
C ion type with the neutral loss of an ammonia group.
Precursor ion type with the neutral loss of a molecule water.
Precursor ion type with the neutral loss of an ammonia group.
The name of the sample labelled with iTRAQ reagent 113
The name of the sample labelled with iTRAQ reagent 118
The name of the sample labelled with iTRAQ reagent 119
The name of the sample labelled with iTRAQ reagent 121
The intensity of the sample labelled with iTRAQ reagent 113
The intensity of the sample labelled with iTRAQ reagent 118
The intensity of the sample labelled with iTRAQ reagent 119
The intensity of the sample labelled with iTRAQ reagent 121
Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page.
SloMo score threshold for valid modification location
MaxQuant percentage threshold for valid modification location
Enzyme that is selected as a parameter of the search engine.
Fixed type of post-translational modification.
Variable type of post-translational modification.
The Sf score for each peptide is calculated by a neural network algorithm that incorporates teh Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and the number of matched peptides for the search. The protein Sf score is the sum of peptide Sf scores for all the peptides associated with that protein.
The name of the sample labelled with TMT reagent 126
The name of the sample labelled with TMT reagent 127
The name of the sample labelled with TMT reagent 128
The name of the sample labelled with TMT reagent 129
The name of the sample labelled with TMT reagent 130
The name of the sample labelled with TMT reagent 131
The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS]
The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS]
The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS]
The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS]
The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS]
The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS]
Name of the gene that has been identified (if a nucleotide database was used to perform the search)
Position of the modification in the protein sequence
Modification Position in Protein Sequence
The original submitted protein accession for this identification. This might have been curated as part of the submission process.
The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication.
Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
Indicates that this protein identification comes from the used decoy database.
The gel's identifier. This identifier should resemble the one used in, for example, the associated publication.
Defines a gel-based proteomics experiment.
Describes gel-based quantification methods
Describes gel-free quantification methods
Describes quantification techniques using isotope labeling
Describes quantification techniques based on selected / multiple reaction monitoring
Describes label free quantification techniques.
Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level
Tandem Mass Tag is a MS2 based isotope labeling quantification technique
Stable isotope labeling with amino acids in cell culture
Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification
Describes isotope labeling quantification techniques detectable at MS1 level.
The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen.
Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements.
AQUA is an isotope labeling based quantification technique that uses known peptides.
Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses.
Exponentially Modified Protein Abundance Index
The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result.
The Total Ion Current (TIC) can be measured or calculated in order to target specific ions.
The heavy label used in SILAC experiments.
The light reagent used in SILAC experiments.
The medium weight reagent used in SILAC experiments.
A unit describing values that can only be interpreted within the same spectrum but cannot be compared to values found in other spectra and or experiments.
Quantification values reported as arbitrary counts (most often ion counts).
Parameters to report quantification values.
Parameters describing quantification values for multiplexed samples.
Values from other quantification techniques.
The Total Ion Count for the given entity.
Identifies samples that are made up of multiplexed subsamples.
Unit used to report quantification results.
Unit to report relative quantification results.
Unit used to describe absolute quantification results.
Quantification results represent ratios.
Quantification results are reported as copies per cell.
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.
The allowed value-type for this CV term.
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
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).
Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (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
The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet.
Dataset that has not been peer-reviewed by any means.
The PX dataset is supported by and is available through the submission repository.
The PX dataset is not fully supported by the submission repository.
Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself.
B ion type with a neutral loss of a phosphate molecule.
B ion type with a neutral loss of 2 phosphate molecules.
B ion type with a neutral loss of 3 phosphate molecules.
Y ion type with a neutral loss of a phosphate molecule.
Y ion type with a neutral loss of 2 phosphate molecules.
Y ion type with a neutral loss of 3 phosphate molecules.
MS1 intensity based label-free quantification method
The basic mass spectrometry strategy used in the experiment.
Mass spectrometry proteomics experimental strategy
Proteins enter directly the mass spectrometer.
Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer.
Bottom-up MS/MS shotgun experiment with data-dependent acquisition, using nomenclature in PMID 20622845, the method of choice for the a priori identification of the protein components of complex samples.
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) to provide information about protein folding and protein-protein interaction.
Chemical cross-linking coupled with mass spectrometry proteomics
Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction.
Affinity purification coupled with mass spectrometry proteomics
A dataset which has an associated manuscript pending for publication.
Labeled reagents used for quantification.
An unlabeled sample used for quantification.
Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140.
Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140
Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140
Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140
The spectrum count is normalized for protein length. Method reviewed in PMID 22772140
Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140
Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140
The NCBI FTP location of the original Sample - Experiment level Peptidome submission data.
Original NCBI Peptidome submission files
Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system).
It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc).
Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243.
ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725.
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.
Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846.
Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610.
Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061.
Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720.
MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777.
Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction.
Protein-protein cross-linking experiment
Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction.
Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method.
Studying all protein samples of diverse host environments like the human body, soil or sea water.
Investigating both human host proteins and associated microbial proteins at the same time from human samples.
"Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies."
Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples.
Waters data independent acquisition method.
Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission).
URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission).
URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission).
URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission).
PRIDE File Properties for all type of files.
Minimum charge for all precursor in the file.
Maximum charge for all precursor in the file.
Minimum precursor mass to charge in the file.
Maximum precursor mass to charge in the file.
Total number of MS3 spectra in the file.
The result analysis parameters is a term to group all the parameters for proteomics data analysis.
Result analysis parameters share by multiple search engine and Quantiative tools.
Minimum charge of precursor to be search.
Maximum charge of precursor to be search.
Min Retention time for precursor to be search.
Max peptide amino acid length for search.
Minimum peptide amino acid length for search.
Min precursor MZ (mass) for precursor to search.
Max precursor MZ (mass) for precursor to search.
Min number of peaks in the spectrum to be search.
Accession or Code of the individual in the sample.
Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment.
Total number of identified peptides in an experiment or assay.
The total number of peptides identified with post-translational modifications.
Total number of reported identified Peptide Spectrum matches (PSMs)
MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring.
Example description of such experiments in 10.1002/pmic.201000578
Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings.
Example description of such samples in 10.1002/pmic.201000578
QC1 sample as described in 10.1371/journal.pone.0189209.
QC2 sample as described in 10.1371/journal.pone.0189209.
Umbrella term for different types of fractionation methods.
Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030).
An electrophoresis method for the separation of amphoteric analytes according to their isoelectric points by the application of an electric field along a pH gradient.
Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity.
Hydrophilic interaction chromatography (HILIC)
Electrostatic repulsion hydrophilic interaction chromatography (ERLIC). Hydrophilic interaction chromatography where the chromatography column is an ion-exchange column and the mobile phase is predominantly organic.
A chromatography method where the separation is caused by differences in ion-exchange affinity.
A chromatography method where the separation is caused by differences in molecular size.
A chromatography method with the stationary phase being a strong anion exchanger.
Strong anion-exchange chromatography (SAX)
A chromatography method with the stationary phase being a weak anion exchanger.
Weak anion-exchange chromatography (WAX)
A chromatography method with the stationary phase being a weak cation exchanger.
Weak cation-exchange chromatography (WCX)
A chromatography method with the stationary phase being a strong cation exchanger.
Strong cation-exchange chromatography (SCX)
Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography.
Liquid chromatography where the mobile phase is significantly more polar than the stationary phase.
Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase.
High-pH reversed-phase chromatography (hpHRP)
Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high.
An electrophoresis method with significantly higher resolution than common isoelectric focusing methods.
High-resolution isoelectric focusing (HiRIEF)
SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel
2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal)
A software that perform protein quantification using mass spectrometry data.
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
A software that perform peptide/protein identification using mass spectrometry 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.
Threshold at precursor level to compare experimental mass with theoretical mass
Threshold at fragment level to compare experimental mass with theoretical mass
The bound fraction after a depletion process
The depleted fraction after a depletion process
Enrichment of specific post-translational modifications
Enrichment method Enrichment of specific post-translational modifications
The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides
Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples
A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy).
beam-type collision-induced dissociation
The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds
The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da
The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da
The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da
The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da
The chemical reagent that is used to break disulfide bonds in proteins
The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2
The reduction agent with chemincal formuls C9H15O6P
The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS
The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)
The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)
The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)
The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)
The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)
The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)
The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)
The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4).
The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2).
Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics
Spectra Cluster Maximum Ratio for the cluster
The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes.
Refer to technologies like SomaScan that employ aptamers as the binding agents for protein detection. SomaScan utilizes Slow Off-rate Modified Aptamers (SOMAmers) for protein targeting and measurement.
Refer to technologies like Olink that utilize antibodies as the primary binding agents for protein detection. Olink's Proximity Extension Assay (PEA) technology relies on using antibody pairs to generate protein-specific signals.
Fragmentation method used for dissociation or fragmentation for MS2
Fragmentation method used for dissociation or fragmentation for MS3
Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome.
Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
Absolute quantification precisely measures the concentration of a specific analyte in a sample
Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples