Proteomics Identification Database Ontology, terms describing proteomics data and experimental metadata
Proteomics Identification Database Ontology
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URL: http://purl.obolibrary.org/obo/pride/pride_cv.obo
The regular course of eating and drinking adopted by a person or animal.
Measurements of the height, weight, length, area, etc., of the human and animal body or its parts.
A quantification of some aspect of the genome, e.g. copy number variation at some locus.
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
A human biological structure, fluid or other substance; excludes single molecular entities.
Anatomic Structure, System, or Substance
The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions.
A grouping of occupations and fields of study.
A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
A symbol or combination of symbols which is assigned to the members of a collection.
A measure of the average kinetic energy of a system of particles.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
An area of database record, or graphical user interface form, into which a particular item of data is entered.
The date on which data creation began [NCI]
Any of the occasions for eating food that occur by custom or habit at more or less fixed times.
Root node for terms relating to Reference additional parameters
Root node for terms relating to the description of a protocol as ordered steps
Protocol step description additional parameter
Root node for terms relating to the description of a ModificationItem
Root node for terms relating to the description of a PeptideItem
Root node for terms relating to the description of an Identification
Root node for terms relating to the description of a Gel parameter
Root node for terms relating to the description of an Experiment
Version number or identifier for search engine
Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification
Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass
Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches
MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)
A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data
XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST
XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics
XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis
Root term for parameters in the context of ExperimentCollection
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
Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins
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 or ontology
PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)
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
A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope
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
Database used to search the protein sequence
The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes
Valid value for the cvLabel entry referencing FIX
A method used to retrieve specific data from a collection of data, based on a given criterion
Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics
Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics
X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics
Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database
The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database
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
A companion tool often used for processing and analyzing mass spectrometry data
File is a digital container used to store information on a computer or other electronic device
The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer
Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment
It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others
A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes
A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt
Any sequence reported before the start of the peptide
Any sequence reported after the end of the peptide sequence
Referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details
Referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)
Score as defined for the Mascot search algorithm
Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database
Fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used
Variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein
The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion
It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis
The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen
The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule
The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search
The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes
Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision
Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements
The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis
The mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm)
Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values
Mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value
Mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage
Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode
Protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton
Protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion
Rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications
The output of a peptide search engine where every peptide in a sample has been identified and matched against a database
All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database
Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database
Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database
Reported chromosome is the chromosomal location of the protein or peptide that has been identified
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
Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters
Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis
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
PepSplice precision refers to the accuracy of peptide-spectrum matches (PSMs) produced by the PepSplice search engine, a specialized tool used for the identification of peptides, particularly for novel or unexpected peptide sequences. Precision is a key metric used to assess the quality and reliability of search results in proteomics
PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results
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'
It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data
MS/MS Search refers to the process of identifying molecules (typically proteins, peptides, metabolites, or small molecules) using tandem mass spectrometry (MS/MS) data. Unlike simple mass spectrometry (MS1), MS/MS involves fragmenting precursor ions into smaller product ions, generating a detailed fragmentation pattern or spectra that can be used to identify the structure or sequence of the molecule
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
A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order
The start position of a nucleic acid sequence on a chromosome refers to the location or coordinate where the sequence begins within the linear structure of a chromosome
Start position of the nucleic acid sequence on the chromosome
The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome
Stop position of the nucleic acid sequence on the chromosome
A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication
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
A protocol step to select for a particular type of peptides
Search parameter that allows users to find query results from old data
Product ion retention time error in minutes
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
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
The SloMo score threshold for a valid modification location is a statistical cutoff used in mass spectrometry (MS/MS) to determine the confidence that a specific position within a peptide or protein is modified
SloMo score threshold for valid modification location
In MaxQuant, the percentage threshold for a valid modification location is typically based on the site probability for post-translational modification (PTM) localization. This probability indicates the confidence that a particular amino acid (residue) within a peptide is modified
MaxQuant percentage threshold for valid modification location
The SloMo score is a quantitative measure used in mass spectrometry (MS/MS) for the localization of modification sites within a peptide or protein sequence
It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide
A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified
A processing method refers to the specific steps or algorithms used to analyze raw MS data, identify peptides, and assign modifications. These processing methods often come with additional parameters that allow users to customize the analysis based on their experimental needs
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
It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses
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 is a MS1 based istope labeling technique for quantification
Stable isotope labeling with amino acids in cell culture
Describes isotope labeling quantification techniques detectable at MS1 level
Describes isotope labeling quantification techniques detectable at MS2 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
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
Exponentially Modified Protein Abundance Index
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)
The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents
The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling
ICPL_0 reagent is a crucial component in the ICPL methodology, serving as the light isotopic label that provides a reference point for quantitative proteomic analyses
ICPLn4 reagent is a specific labeling compound that incorporates four deuterium (^2H) atoms, resulting in a mass shift of approximately 4.0251 Da per labeled amino acid compared to the light ICPL_0 reagent
The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group
The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group
Parameters to report quantification values
Parameters describing quantification values for multiplexed samples
Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest
Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
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 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
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
A 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 a 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
A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples
MS1 intensity based label-free quantification method
The basic mass spectrometry strategy used in the experiment
Mass spectrometry proteomics experimental strategy
A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)
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 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
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
Result analysis parameters specific to a search engine or quantitative tool
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
Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings
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
Umbrella term for different types of separation 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
URI of one external file associated to the PRIDE experiment on SDRF files definitions
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
Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology
Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies
SelexION differential mobility separation device
The technology type or platform used to perform the study
An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry
proteomic profiling by mass spectrometry
Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications
TMT 10-plex labeling kit has 10 channels
TMT 16-plex labeling kit has 16 channels
TMT 18-plex labeling kit has 18 channels
Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology
Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology
The Olink Explore HT is a high-throughput proteomics platform for large-scale biomarker discovery, enabling simultaneous measurement of thousands of proteins from minimal sample volumes
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome.
A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107
Name of the project within which the sequencing was organized. MIXS:0000092
History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280
History of liver disorders; can include multiple disorders. MIXS:0000282
Specification of special diet; can include multiple special diets. MIXS:0000905
A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861
Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255
List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031
Can include multiple medication codes. MIXS:0000884
List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751
Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867
Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888
Total mass of the host at collection, the unit depends on host. MIXS:0000263
Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869
Content of last meal and time since feeding; can include multiple values. MIXS:0000870
Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872
Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274
Core body temperature of the host when sample was collected. MIXS:0000874
Body mass index, calculated as weight/(height)squared. MIXS:0000317
A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895
Most frequent job performed by subject. MIXS:0000896
Whether full medical history was collected. MIXS:0000897
Resting pulse, measured as beats per minutes. MIXS:0000333
Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754
The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. MIXS:0000183
Oxygenation status of the sample. MIXS:0000753
Temperature of the sample at the time of sampling. MIXS:0000113
Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). MIXS:0000103
Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110
Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111
sample volume or weight for DNA extraction
Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116
The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298
Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755
Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752
The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples MIXS:0000018
Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit MIXS:0000093
Present state of sample site MIXS:0001080
Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312
Reference or method used in vegetation classification MIXS:0000314
Previous land use and dates MIXS:0000315
Reference or method used in determining previous land use and dates MIXS:0000316
Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318
Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639
Note method(s) used for tilling MIXS:0001081
Historical and/or physical evidence of fire MIXS:0001086
Historical and/or physical evidence of flooding MIXS:0000319
Unusual physical events that may have affected microbial populations MIXS:0000320
Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath MIXS:0001082
Reference or method used in determining the horizon MIXS:0000321
Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322
Reference or method used in determining the water content of soil MIXS:0000323
Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325
Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327
The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000644
The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000645
Link to digitized soil maps or other soil classification information MIXS:0000329
Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution MIXS:0001083
Soil classification based on local soil classification system MIXS:0000330
Reference or method used in determining the local soil classification MIXS:0000331
soil taxonomic of local classification method
Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer MIXS:0000646
The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration MIXS:0000647
Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084
Drainage classification from a standard system such as the USDA system MIXS:0001085
The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional MIXS:0000335
Reference or method used in determining soil texture MIXS:0000336
Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001
Reference or method used in determining pH MIXS:0001106
Concentration of organic matter MIXS:0000204
Total organic carbon content MIXS:0000533
Reference or method used in determining total organic carbon MIXS:0000337
Total nitrogen content of the sample MIXS:0000530
Reference or method used in determining the total nitrogen MIXS:0000338
The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units MIXS:0000650
Reference or method used in determining microbial biomass MIXS:0000339
Link to additional analysis results performed on the sample MIXS:0000340
Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652
extreme unusual properties of heavy metals
Reference or method used in determining heavy metals MIXS:0000343
extreme unusual properties of heavy metals method
Aluminum saturation (esp. For tropical soils) MIXS:0000607
extreme unusual properties of AI saturation
Reference or method used in determining Al saturation MIXS:0000324
extreme unusual properties of AI saturation method
Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421
Method used for alkalinity measurement MIXS:0000298
Concentration of alkyl diethers MIXS:0000490
Measurement of aminopeptidase activity MIXS:0000172
Concentration of ammonium in the sample MIXS:0000427
Measurement of atmospheric data; can include multiple data MIXS:0001097
Measurement of bacterial carbon production MIXS:0000173
Bacterial production in the water column measured by isotope uptake MIXS:0000683
Measurement of bacterial respiration in the water column MIXS:0000684
Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174
Concentration of bishomohopanol MIXS:0000175
Concentration of calcium in the sample MIXS:0000432
Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310
Concentration of chloride in the sample MIXS:0000429
Concentration of chlorophyll MIXS:0000177
Electrical conductivity of water MIXS:0000692
Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435
Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178
Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436
Concentration of dissolved hydrogen MIXS:0000179
Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434
Concentration of dissolved inorganic nitrogen MIXS:0000698
Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106
Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433
Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162
Concentration of dissolved oxygen MIXS:0000119
Visible waveband radiance and irradiance measurements in the water column MIXS:0000703
Raw or converted fluorescence of water MIXS:0000704
Measurement of glucosidase activity MIXS:0000137
Measurement of light intensity MIXS:0000706
Concentration of magnesium in the sample MIXS:0000431
Measurement of mean friction velocity MIXS:0000498
Measurement of mean peak friction velocity MIXS:0000502
Concentration of nitrate in the sample MIXS:0000425
Concentration of nitrite in the sample MIXS:0000426
Concentration of nitrogen (total) MIXS:0000504
Concentration of organic carbon MIXS:0000508
Concentration of organic nitrogen MIXS:0000205
Concentration of particulate organic carbon MIXS:0000515
Concentration of particulate organic nitrogen MIXS:0000719
Concentration of petroleum hydrocarbon MIXS:0000516
Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180
Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181
Concentration of potassium in the sample MIXS:0000430
Pressure to which the sample is subject to, in atmospheres MIXS:0000412
Measurement of primary production, generally measured as isotope uptake MIXS:0000728
Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182
Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample MIXS:0000735
Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample MIXS:0000736
Sodium concentration in the sample MIXS:0000428
Concentration of soluble reactive phosphorus MIXS:0000738
Concentration of sulfate in the sample MIXS:0000423
Concentration of sulfide in the sample MIXS:0000424
Concentration of suspended particulate matter MIXS:0000741
Measurement of total depth of water column MIXS:0000634
Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744
Total inorganic nitrogen content MIXS:0000745
Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen MIXS:0000102
Total particulate carbon content MIXS:0000747
Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117
Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191
A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium
A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment
Olink Reveal is an NGS-based proteomics platform that measures approximately 1,000 proteins with high sensitivity from just 4 µL of sample, using standard lab equipment, with a focus on immune and inflammation markers
A defined organization or layout representing and structuring data in a file. The file format specifies how information is encoded, stored, and interpreted within the file.
A checklist of columns and properties that will be applied during a validation process to an SDRF or other PSI standard
A hash generated after validating an SDRF dataset; this is helpful to understand if one file has been validated or not
An accession to a cellosaurus cell line that could be use to annotate SDRF samples
A name to a cellosaurus cell line that could be use to annotate SDRF samples