Deepti Jaiswal Kundu Nithu Sara John Yasset Perez-Riverol Proteomics Identification Database Ontology, terms describing proteomics data and experimental metadata Proteomics Identification Database Ontology * PRIDE:$sequence(7,0,9999999)$ 14:01:2026 10:00 PRIDE 1.4 Yasset Perez-Riverol This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ URL: http://purl.obolibrary.org/obo/pride/pride_cv.obo definition namespace-id-rule database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace has_related_synonym id The regular course of eating and drinking adopted by a person or animal. PRIDE EFO:0002755 diet The regular course of eating and drinking adopted by a person or animal. EFO:EFO Measurements of the height, weight, length, area, etc., of the human and animal body or its parts. PRIDE EFO:0004324 body weights and measures Measurements of the height, weight, length, area, etc., of the human and animal body or its parts. EFO:EFO A quantification of some aspect of the genome, e.g. copy number variation at some locus. PRIDE EFO:0004554 genomic measurement A quantification of some aspect of the genome, e.g. copy number variation at some locus. EFO:EFO Fragmentation method used for dissociation or fragmentation PRIDE MS:1000044 dissociation method Fragmentation method used for dissociation or fragmentation PRIDE:PRIDE Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion PRIDE MS:1000045 collision energy Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion PRIDE:PRIDE Mass analyzer PRIDE MS:1000451 mass analyzer Mass analyzer PRIDE:PRIDE A sample that has not been labelled or modified PRIDE MS:1002038 label free sample A sample that has not been labelled or modified PRIDE:PRIDE A human biological structure, fluid or other substance; excludes single molecular entities. PRIDE NCIT:C12219 Anatomic Structure, System, or Substance A human biological structure, fluid or other substance; excludes single molecular entities. NCI 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. PRIDE NCIT:C16205 Healthcare Activity 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. NCI A grouping of occupations and fields of study. PRIDE NCIT:C19160 Occupation or Discipline A grouping of occupations and fields of study. NCI A distinguishing quality or prominent aspect of a person, object, action, process, or substance. PRIDE NCIT:C20189 Property or Attribute A distinguishing quality or prominent aspect of a person, object, action, process, or substance. NCI A symbol or combination of symbols which is assigned to the members of a collection. PRIDE NCIT:C25162 Code A symbol or combination of symbols which is assigned to the members of a collection. NCI A measure of the average kinetic energy of a system of particles. PRIDE NCIT:C25206 Temperature A measure of the average kinetic energy of a system of particles. NCI The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. PRIDE NCIT:C25347 Height The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. NCI The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. PRIDE NCIT:C25447 Characteristic The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. NCI An area of database record, or graphical user interface form, into which a particular item of data is entered. PRIDE NCIT:C25507 Data Field An area of database record, or graphical user interface form, into which a particular item of data is entered. NCI A written record of events. PRIDE NCIT:C45279 Log A written record of events. NCI The date on which data creation began [NCI] PRIDE NCIT:C69199 Content Creation date The date on which data creation began [NCI] PRIDE:PRIDE Any of the occasions for eating food that occur by custom or habit at more or less fixed times. PRIDE NCIT:C80248 Meal Any of the occasions for eating food that occur by custom or habit at more or less fixed times. NCI Root node for terms relating to Reference additional parameters PRIDE PRIDE:0000000 Reference additional parameter Root node for terms relating to Reference additional parameters PRIDE:PRIDE Root node for terms relating to the description of a protocol as ordered steps PRIDE PRIDE:0000001 Protocol step description additional parameter Root node for terms relating to the description of a protocol as ordered steps PRIDE:PRIDE Root node for terms relating to the description of a ModificationItem PRIDE PRIDE:0000002 ModificationItem additional parameter Root node for terms relating to the description of a ModificationItem PRIDE:PRIDE Root node for terms relating to the description of a PeptideItem PRIDE PRIDE:0000003 Peptide item additional parameter Root node for terms relating to the description of a PeptideItem PRIDE:PRIDE Root node for terms relating to the description of an Identification PRIDE PRIDE:0000004 Identification additional parameter Root node for terms relating to the description of an Identification PRIDE:PRIDE Root node for terms relating to the description of a Gel parameter PRIDE PRIDE:0000005 Gel additional parameter Root node for terms relating to the description of a Gel parameter PRIDE:PRIDE Root node for terms relating to the description of an Experiment PRIDE PRIDE:0000006 Experiment additional parameter Root node for terms relating to the description of an Experiment PRIDE:PRIDE Version number or identifier for search engine PRIDE PRIDE:0000007 SearchEngineVersion Version number or identifier for search engine PRIDE:PRIDE Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification PRIDE PRIDE:0000008 Protein search engine output parameter Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification PRIDE:PRIDE Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass PRIDE PRIDE:0000009 Ion mass tolerance Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass PRIDE:PRIDE 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 PRIDE PRIDE:0000010 Precursor ion mass tolerance 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 PRIDE:PRIDE 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) PRIDE PRIDE:0000011 MS2 ion mass tolerance 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) PRIDE:PRIDE 1.0 - normalized correlation score PRIDE PRIDE:0000012 Delta Cn 1.0 - normalized correlation score PRIDE:PRIDE A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data PRIDE PRIDE:0000013 X correlation A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data PRIDE:PRIDE XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST PRIDE PRIDE:0000014 X correlation (+1) XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST PRIDE:PRIDE XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics PRIDE PRIDE:0000015 X correlation (+2) XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics PRIDE:PRIDE XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis PRIDE PRIDE:0000016 X correlation (+3) XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis PRIDE:PRIDE Root term for parameters in the context of ExperimentCollection PRIDE PRIDE:0000017 Sample description additional parameter Root term for parameters in the context of ExperimentCollection PRIDE:PRIDE 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 PRIDE PRIDE:0000018 Disease free 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 PRIDE:PRIDE To make something soluble or more soluble, especially in water, by the action of a detergent or other agent PRIDE PRIDE:0000019 Solubilization To make something soluble or more soluble, especially in water, by the action of a detergent or other agent PRIDE:PRIDE The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components PRIDE PRIDE:0000020 Depletion The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components PRIDE:PRIDE 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) PRIDE PRIDE:0000021 Fractionation 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) PRIDE:PRIDE To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time PRIDE PRIDE:0000022 Separation To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time PRIDE:PRIDE The removal of a region of a gel which contains protein(s) of interest PRIDE PRIDE:0000023 Band excision The removal of a region of a gel which contains protein(s) of interest PRIDE:PRIDE The fragmentation of proteins into peptides through the use of an enzyme such as Trypsin PRIDE PRIDE:0000024 Enzyme digestion The fragmentation of proteins into peptides through the use of an enzyme such as Trypsin PRIDE:PRIDE Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins PRIDE PRIDE:0000025 Reduction Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins PRIDE:PRIDE The transfer of an alkyl group from one molecule to another PRIDE PRIDE:0000026 Alkylation The transfer of an alkyl group from one molecule to another PRIDE:PRIDE 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 PRIDE PRIDE:0000027 Mass spectrometry 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 PRIDE:PRIDE Valid values for cvLabel entries referencing external database or ontology PRIDE PRIDE:0000028 Cv Label Valid values for cvLabel entries referencing external database or ontology PRIDE:PRIDE PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM) PRIDE PRIDE:0000029 PubMed PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM) PRIDE:PRIDE Valid value for the cvLabel entry referencing PRIDE PRIDE PRIDE:0000030 PRIDE Valid value for the cvLabel entry referencing PRIDE PRIDE:PRIDE Valid value for the cvLabel entry referencing GO PRIDE PRIDE:0000031 GO Valid value for the cvLabel entry referencing GO PRIDE:PRIDE Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH) PRIDE PRIDE:0000032 MeSH Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH) PRIDE:PRIDE Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy PRIDE PRIDE:0000033 NEWT Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy PRIDE:PRIDE Valid value for the cvLabel entry referencing the PSI ontology PRIDE PRIDE:0000034 PSI Valid value for the cvLabel entry referencing the PSI ontology PRIDE:PRIDE Valid value for the cvLabel entry referencing UNIMOD PRIDE PRIDE:0000035 UNIMOD Valid value for the cvLabel entry referencing UNIMOD PRIDE:PRIDE Valid value for the cvLabel entry referencing RESID PRIDE PRIDE:0000036 RESID Valid value for the cvLabel entry referencing RESID PRIDE:PRIDE A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope PRIDE PRIDE:0000037 Staining A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope PRIDE:PRIDE Valid value for the cvLabel entry referencing ISBN PRIDE PRIDE:0000038 ISBN Valid value for the cvLabel entry referencing ISBN PRIDE:PRIDE Any technique which separates differentiated structures from the cell PRIDE PRIDE:0000039 Organelle isolation Any technique which separates differentiated structures from the cell PRIDE:PRIDE This CV term should be used in association with a value that is a free-text description of the experiment PRIDE PRIDE:0000040 Experiment description This CV term should be used in association with a value that is a free-text description of the experiment PRIDE:PRIDE Database used to search the protein sequence PRIDE PRIDE:0000041 Search database protein sequence Database used to search the protein sequence PRIDE:PRIDE The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes PRIDE PRIDE:0000042 DOI The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes PRIDE:PRIDE Valid value for the cvLabel entry referencing FIX PRIDE PRIDE:0000043 FIX Valid value for the cvLabel entry referencing FIX PRIDE:PRIDE A method used to retrieve specific data from a collection of data, based on a given criterion PRIDE PRIDE:0000044 Search algorithm A method used to retrieve specific data from a collection of data, based on a given criterion PRIDE:PRIDE Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics PRIDE PRIDE:0000045 Sequest Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics PRIDE:PRIDE Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics PRIDE PRIDE:0000046 Mascot Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics PRIDE:PRIDE X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics PRIDE PRIDE:0000047 X X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics PRIDE:PRIDE 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 PRIDE PRIDE:0000048 Output parameter 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000049 Peptide search engine output parameter 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 PRIDE:PRIDE Final correlation score rank and preliminary score rank PRIDE PRIDE:0000050 Rank/Sp Final correlation score rank and preliminary score rank PRIDE:PRIDE M/z of the singly-charged precursor (precursor mass + mass of hydrogen atom) PRIDE PRIDE:0000051 (M+H)+ M/z of the singly-charged precursor (precursor mass + mass of hydrogen atom) PRIDE:PRIDE Normalized correlation score PRIDE PRIDE:0000052 Cn Normalized correlation score PRIDE:PRIDE Raw correlation score (Sequest) PRIDE PRIDE:0000053 Sequest score Raw correlation score (Sequest) PRIDE:PRIDE Preliminary score PRIDE PRIDE:0000054 Sp Preliminary score PRIDE:PRIDE The number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide PRIDE PRIDE:0000055 Ions The number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide PRIDE:PRIDE A companion tool often used for processing and analyzing mass spectrometry data PRIDE PRIDE:0000056 Bioworks A companion tool often used for processing and analyzing mass spectrometry data PRIDE:PRIDE Molecular weight of a protein PRIDE PRIDE:0000057 Molecular weight Molecular weight of a protein PRIDE:PRIDE Bioworks z score PRIDE PRIDE:0000058 z score Bioworks z score PRIDE:PRIDE File is a digital container used to store information on a computer or other electronic device PRIDE PRIDE:0000059 File File is a digital container used to store information on a computer or other electronic device PRIDE:PRIDE 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 PRIDE PRIDE:0000060 Scan 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 PRIDE:PRIDE Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment PRIDE PRIDE:0000061 Coverage Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment PRIDE:PRIDE 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 PRIDE PRIDE:0000062 rsp 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000063 Protein description line 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 PRIDE:PRIDE A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt PRIDE PRIDE:0000064 Secondary accession A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt PRIDE:PRIDE Any sequence reported before the start of the peptide PRIDE PRIDE:0000065 Upstream flanking sequence Any sequence reported before the start of the peptide PRIDE:PRIDE Any sequence reported after the end of the peptide sequence PRIDE PRIDE:0000066 Downstream flanking seqeuence Any sequence reported after the end of the peptide sequence PRIDE:PRIDE 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 PRIDE PRIDE:0000067 Reference reporting this experiment 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 PRIDE:PRIDE 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.) PRIDE PRIDE:0000068 Reference describing sample preparation 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.) PRIDE:PRIDE Score as defined for the Mascot search algorithm PRIDE PRIDE:0000069 Mascot score Score as defined for the Mascot search algorithm PRIDE:PRIDE Cleavage of the peptide bond PRIDE PRIDE:0000070 Peptide cleavage Cleavage of the peptide bond PRIDE:PRIDE 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 PRIDE PRIDE:0000071 Search engine setting 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000072 Fixed modification setting 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000073 Variable modification setting 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 PRIDE:PRIDE The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion PRIDE PRIDE:0000074 Maximum Missed Cleavages Setting The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion PRIDE:PRIDE It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis PRIDE PRIDE:0000075 Mass value type setting It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis PRIDE:PRIDE 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 PRIDE PRIDE:0000076 Mass value type setting monoisotopic 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 PRIDE:PRIDE The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule PRIDE PRIDE:0000077 Mass value type setting average The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule PRIDE:PRIDE 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 PRIDE PRIDE:0000078 Peptide mass tolerance setting 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000079 Accurate mass mode setting 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 PRIDE:PRIDE Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision PRIDE PRIDE:0000080 Accurate mass mode setting true Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision PRIDE:PRIDE Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements PRIDE PRIDE:0000081 Accurate mass mode setting false Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements PRIDE:PRIDE The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis PRIDE PRIDE:0000082 Mass error type setting The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis PRIDE:PRIDE 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) PRIDE PRIDE:0000083 mass error type setting ppm 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) PRIDE:PRIDE Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values PRIDE PRIDE:0000084 mass error type setting mmu Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values PRIDE:PRIDE 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 PRIDE PRIDE:0000085 mass error type setting percent 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000086 mass error type setting Daltons 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 PRIDE:PRIDE Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode PRIDE PRIDE:0000087 Protonated setting Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode PRIDE:PRIDE 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 PRIDE PRIDE:0000088 Protonated setting MH+ 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 PRIDE;PRIDE 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 PRIDE PRIDE:0000090 Protonated setting M-H- 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000091 Rank 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 PRIDE:PRIDE The output of a peptide search engine where every peptide in a sample has been identified and matched against a database PRIDE PRIDE:0000092 All peptides matched The output of a peptide search engine where every peptide in a sample has been identified and matched against a database PRIDE:PRIDE 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 PRIDE PRIDE:0000093 All peptides matched true 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 PRIDE:PRIDE Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database PRIDE PRIDE:0000094 All peptides matched false Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database PRIDE:PRIDE 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 PRIDE PRIDE:0000095 Masses matched 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 PRIDE:PRIDE Reported chromosome is the chromosomal location of the protein or peptide that has been identified PRIDE PRIDE:0000096 Reported Chromosome Reported chromosome is the chromosomal location of the protein or peptide that has been identified PRIDE:PRIDE Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project PRIDE PRIDE:0000097 Project Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project PRIDE:PRIDE 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 PRIDE PRIDE:0000098 Indistinguishable alternative protein accession 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 PRIDE:PRIDE The probability score for this peptide assignment to be correct, as calculated by PeptideProphet PRIDE PRIDE:0000099 PeptideProphet probability score The probability score for this peptide assignment to be correct, as calculated by PeptideProphet PRIDE:PRIDE The probability score for this protein identification to be correct, as calculated by ProteinProphet PRIDE PRIDE:0000100 ProteinProphet probability score The probability score for this protein identification to be correct, as calculated by ProteinProphet PRIDE:PRIDE The PeptideProphet algorithm PRIDE PRIDE:0000101 PeptideProphet The PeptideProphet algorithm PRIDE:PRIDE The ProteinProphet algorithm PRIDE PRIDE:0000102 ProteinProphet The ProteinProphet algorithm PRIDE:PRIDE The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime PRIDE PRIDE:0000103 Gel run date The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime PRIDE:PRIDE The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double PRIDE PRIDE:0000104 Sample volume loaded The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double PRIDE:PRIDE The width of the referenced gel image in pixels. Mandatory value of type xsd:int PRIDE PRIDE:0000105 Width in pixels The width of the referenced gel image in pixels. Mandatory value of type xsd:int PRIDE:PRIDE The height of the referenced gel image in pixels. Mandatory value of type xsd:int PRIDE PRIDE:0000106 Height in pixels The height of the referenced gel image in pixels. Mandatory value of type xsd:int PRIDE:PRIDE Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification PRIDE PRIDE:0000107 Gel spot parameter Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification PRIDE:PRIDE The intensity of the spot on the gel. Mandatory value of type xsd:double PRIDE PRIDE:0000108 Gel spot intensity The intensity of the spot on the gel. Mandatory value of type xsd:double PRIDE:PRIDE The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double PRIDE PRIDE:0000109 Gel spot area The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double PRIDE:PRIDE The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double PRIDE PRIDE:0000110 Gel spot volume The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double PRIDE:PRIDE A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment PRIDE PRIDE:0000111 Reference describing data analysis A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment PRIDE:PRIDE The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included PMF PRIDE PRIDE:0000112 Identified by peptide mass fingerprint The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included PRIDE:PRIDE PMF PRIDE The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching PFF PRIDE PRIDE:0000113 Identified by peptide fragmentation The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching PRIDE:PRIDE PFF PRIDE The name of the sample labelled with iTRAQ reagent 114 PRIDE PRIDE:0000114 iTRAQ reagent 114 The name of the sample labelled with iTRAQ reagent 114 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 115 PRIDE PRIDE:0000115 iTRAQ reagent 115 The name of the sample labelled with iTRAQ reagent 115 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 116 PRIDE PRIDE:0000116 iTRAQ reagent 116 The name of the sample labelled with iTRAQ reagent 116 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 117 PRIDE PRIDE:0000117 iTRAQ reagent 117 The name of the sample labelled with iTRAQ reagent 117 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 114 PRIDE PRIDE:0000118 iTRAQ intensity 114 The intensity of the sample labelled with iTRAQ reagent 114 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 115 PRIDE PRIDE:0000119 iTRAQ intensity 115 The intensity of the sample labelled with iTRAQ reagent 115 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 116 PRIDE PRIDE:0000120 iTRAQ intensity 116 The intensity of the sample labelled with iTRAQ reagent 116 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 117 PRIDE PRIDE:0000121 iTRAQ intensity 117 The intensity of the sample labelled with iTRAQ reagent 117 PRIDE:PRIDE 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 PRIDE PRIDE:0000122 Two Dimensional Polyacrylamide Gel Electrophoresis 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 PRIDE:PRIDE Electrophoresis using an gel which has a pH gradient along its length PRIDE PRIDE:0000123 Immobilized pH Gradient Electrophoresis Electrophoresis using an gel which has a pH gradient along its length PRIDE:PRIDE 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 PRIDE PRIDE:0000124 Sodium dodecyl sulfate polyacrylamide gel electrophoresis 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 PRIDE:PRIDE The lowest pH of an immobilised pH gradient gel PRIDE PRIDE:0000125 pH low value The lowest pH of an immobilised pH gradient gel PRIDE:PRIDE The highest pH of an immobilised pH gradient gel PRIDE PRIDE:0000126 pH high value The highest pH of an immobilised pH gradient gel PRIDE:PRIDE The length in centimeters of an immobilised pH gradient gel PRIDE PRIDE:0000127 IPG strip length cm The length in centimeters of an immobilised pH gradient gel PRIDE:PRIDE Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters PRIDE PRIDE:0000128 First dimension details Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters PRIDE:PRIDE Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis PRIDE PRIDE:0000129 Second dimension details Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis PRIDE:PRIDE A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values PRIDE PRIDE:0000131 Spot normalized volume A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values PRIDE:PRIDE The method by which the normalized value for spot volume is derived from the individual gel spot volume values PRIDE PRIDE:0000132 Spot normalized volume method The method by which the normalized value for spot volume is derived from the individual gel spot volume values PRIDE:PRIDE The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146) PRIDE PRIDE:0000133 Isobaric residue K/Q The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146) PRIDE:PRIDE A substance that prevents coagulation; that is, it stops blood from clotting PRIDE PRIDE:0000134 Anticoagulant A substance that prevents coagulation; that is, it stops blood from clotting PRIDE:PRIDE Date of last mapping of given identifier to current UniProt accession number PRIDE PRIDE:0000135 Mapping date Date of last mapping of given identifier to current UniProt accession number PRIDE:PRIDE 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' PRIDE PRIDE:0000136 Mapping status 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' PRIDE:PRIDE 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' PRIDE PRIDE:0000137 Mapping history 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' PRIDE:PRIDE PeptideProphet discriminant score fval PRIDE PRIDE:0000138 Discriminant score PeptideProphet discriminant score fval PRIDE:PRIDE Error message: SOAP protocol failed PRIDE PRIDE:0000139 Not Mapped SOAP Error Error message: SOAP protocol failed PRIDE:PRIDE Error message: Error with queried database PRIDE PRIDE:0000140 Not Mapped Database Error Error message: Error with queried database PRIDE:PRIDE Error message: Unable to match given identifier PRIDE PRIDE:0000141 Not Mapped No Mapping Found Error message: Unable to match given identifier PRIDE:PRIDE Error message: One or more peptide sequences did not match query sequence PRIDE PRIDE:0000142 Not Mapped Peptide Mismatch Error message: One or more peptide sequences did not match query sequence PRIDE:PRIDE Error message: No mapping to proteins from defined taxon PRIDE PRIDE:0000143 Mapped Taxon Not Found Error message: No mapping to proteins from defined taxon PRIDE:PRIDE Sucessful completion of operation message PRIDE PRIDE:0000144 Mapped All Ok Sucessful completion of operation message PRIDE:PRIDE The PepSplice algorithm PRIDE PRIDE:0000145 PepSplice The PepSplice algorithm PRIDE:PRIDE 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 PRIDE PRIDE:0000146 PepSplice precision 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000147 PepSplice false discovery rate 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 PRIDE:PRIDE A Score based on the hypergeometric model PRIDE PRIDE:0000148 PepSplice P-value A Score based on the hypergeometric model PRIDE:PRIDE The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together PRIDE PRIDE:0000149 PepSplice Deltascore The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together PRIDE:PRIDE The score count PRIDE PRIDE:0000150 PepSplice Score Count The score count PRIDE:PRIDE The Sum of all penalties for the peptide assignment PRIDE PRIDE:0000151 PepSplice Penalty The Sum of all penalties for the peptide assignment PRIDE:PRIDE The reading direction on the DNA PRIDE PRIDE:0000152 PepSplice Read Direction The reading direction on the DNA PRIDE:PRIDE The reading direction on the DNA is 5' to 3' PRIDE PRIDE:0000153 PepSplice Forward Read Direction The reading direction on the DNA is 5' to 3' PRIDE:PRIDE The reading direction on the DNA 3' to 5' PRIDE PRIDE:0000154 PepSplice Reverse Read Direction The reading direction on the DNA 3' to 5' PRIDE:PRIDE Unsucessful mapping PRIDE PRIDE:0000155 Unmappable Unsucessful mapping PRIDE:PRIDE Unique identifier of project Project Identifier PRIDE PRIDE:0000156 Project identifier Unique identifier of project PRIDE:PRIDE Project Identifier NCIT Type of search PRIDE PRIDE:0000157 Search type Type of search PRIDE:PRIDE It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data PRIDE PRIDE:0000158 MS search It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data PRIDE:PRIDE 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 PRIDE PRIDE:0000159 MS/MS search 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 PRIDE:PRIDE Type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g PRIDE PRIDE:0000160 Enzyme Type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g PRIDE:PRIDE Range of acceptable fragment masses accepted by instrument PRIDE PRIDE:0000161 Fragment mass tolerance setting Range of acceptable fragment masses accepted by instrument PRIDE:PRIDE Number of missed cleavage sites taken into account PRIDE PRIDE:0000162 Allowed missed cleavages Number of missed cleavage sites taken into account PRIDE:PRIDE Name of instrument used in analysis PRIDE PRIDE:0000163 Instrument type Name of instrument used in analysis PRIDE:PRIDE Sucessful mapping without supporting evidence from peptides PRIDE PRIDE:0000164 Mapped Without Supporting Peptides Sucessful mapping without supporting evidence from peptides PRIDE:PRIDE PICR tool has allocated the accession number PRIDE PRIDE:0000165 Automatic allocation PICR tool has allocated the accession number PRIDE:PRIDE Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist PRIDE PRIDE:0000166 Ambiguous modification Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist PRIDE:PRIDE Detailed information about a genomic locus identified by whole genome searches PRIDE PRIDE:0000167 Novel locus information Detailed information about a genomic locus identified by whole genome searches PRIDE:PRIDE A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order PRIDE PRIDE:0000168 Nucleic acid sequence A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order PRIDE:PRIDE 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 PRIDE PRIDE:0000169 Start position of the nucleic acid sequence on the chromosome 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 PRIDE:PRIDE The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome PRIDE PRIDE:0000170 Stop 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 PRIDE:PRIDE A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication PRIDE PRIDE:0000171 funding reference A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication PRIDE:PRIDE Value of average of all individual peptide identifications for this protein PRIDE PRIDE:0000172 Search database protein sequence length Value of average of all individual peptide identifications for this protein PRIDE:PRIDE Value of average of all individual peptide scores PRIDE PRIDE:0000173 MeanOfPeptideScores Value of average of all individual peptide scores PRIDE:PRIDE Isoelectric point of a protein pI PRIDE PRIDE:0000174 Isoelectric point Isoelectric point of a protein PRIDE:PRIDE pI PRIDE The software which was used to generate the PRIDE XML file PRIDE PRIDE:0000175 XML generation software The software which was used to generate the PRIDE XML file PRIDE:PRIDE The X!Tandem hyperscore for the peptide PRIDE PRIDE:0000176 X!Tandem Hyperscore The X!Tandem hyperscore for the peptide PRIDE:PRIDE The Spectrum Mill score for the peptide PRIDE PRIDE:0000177 Spectrum Mill peptide score The Spectrum Mill score for the peptide PRIDE:PRIDE A protocol step to select for a particular type of peptides PRIDE PRIDE:0000178 Peptide selection A protocol step to select for a particular type of peptides PRIDE:PRIDE X|Tandem dot product score PRIDE PRIDE:0000179 dotproduct X|Tandem dot product score PRIDE:PRIDE X|Tandem delta score PRIDE PRIDE:0000180 delta X|Tandem delta score PRIDE:PRIDE X|Tandem delta star score PRIDE PRIDE:0000181 deltastar X|Tandem delta star score PRIDE:PRIDE X|Tandem Z score PRIDE PRIDE:0000182 zscore X|Tandem Z score PRIDE:PRIDE X|Tandem expectancy score PRIDE PRIDE:0000183 expect X|Tandem expectancy score PRIDE:PRIDE Search parameter that allows users to find query results from old data PRIDE PRIDE:0000184 Query number Search parameter that allows users to find query results from old data PRIDE:PRIDE E-value parameter from OMSSA PRIDE PRIDE:0000185 OMSSA E-value E-value parameter from OMSSA PRIDE:PRIDE P-value parameter from OMSSA PRIDE PRIDE:0000186 OMSSA P-value P-value parameter from OMSSA PRIDE:PRIDE Fragment ion annotation of the peptide Product ion property PRIDE PRIDE:0000187 Fragment Ion Annotation Fragment ion annotation of the peptide PRIDE:PRIDE Product ion property PRIDE Mass Fragment ion mass PRIDE PRIDE:0000188 product ion m/z Mass PRIDE:PRIDE Fragment ion mass PRIDE Intensity Fragment ion intensity PRIDE PRIDE:0000189 product ion intensity Intensity PRIDE Fragment ion intensity PRIDE Mass error Fragment ion mass error PRIDE PRIDE:0000190 product ion mass error Mass error PRIDE:PRIDE Fragment ion mass error PRIDE Product ion retention time error in minutes Fragment ion retention time error PRIDE PRIDE:0000191 product ion retention time error Product ion retention time error in minutes PRIDE:PRIDE Fragment ion retention time error PRIDE Product ion type Fragment ion type PRIDE PRIDE:0000192 product ion type Product ion type PRIDE:PRIDE Fragment ion type PRIDE Y ion type y fragment ion PRIDE PRIDE:0000193 y ion Y ion type PRIDE:PRIDE y fragment ion PRIDE B ion type b fragment ion PRIDE PRIDE:0000194 b ion B ion type PRIDE:PRIDE b fragment ion PRIDE B ion type with a neutral loss of an ammonia group b fragment ion -NH3 PRIDE PRIDE:0000195 b ion -NH3 B ion type with a neutral loss of an ammonia group PRIDE:PRIDE b fragment ion -NH3 PRIDE B ion type with a neutral loss of a water molecule b fragment ion -H2O PRIDE PRIDE:0000196 b ion -H2O B ion type with a neutral loss of a water molecule PRIDE:PRIDE b fragment ion -H2O PRIDE Y ion type with the neutral loss of a molecule water y fragment ion -H2O PRIDE PRIDE:0000197 y ion -H2O Y ion type with the neutral loss of a molecule water PRIDE:PRIDE y fragment ion -H2O PRIDE Y ion type with the neutral loss of an ammonia group y fragment ion -NH3 PRIDE PRIDE:0000198 y ion -NH3 Y ion type with the neutral loss of an ammonia group PRIDE:PRIDE y fragment ion -NH3 PRIDE Ion resulting from in-source fragmentation In source fragment ion In-source ion PRIDE PRIDE:0000199 in source ion Ion resulting from in-source fragmentation PRIDE:PRIDE In source fragment ion PRIDE In-source ion PRIDE Fragment ion that could not be assigned to a predicted fragment ion mass unidentified ion PRIDE PRIDE:0000200 non-identified ion Fragment ion that could not be assigned to a predicted fragment ion mass PRIDE:PRIDE unidentified ion PRIDE Fragment ion that was matched to another, co-eluting peptide precursor PRIDE PRIDE:0000201 co-eluting ion Fragment ion that was matched to another, co-eluting peptide precursor PRIDE:PRIDE Parent ion annotation of the peptide PRIDE PRIDE:0000202 Parent Ion Annotation Parent ion annotation of the peptide PRIDE:PRIDE Retention time in minutes PRIDE PRIDE:0000203 parent ion retention time Retention time in minutes PRIDE:PRIDE Charge state Fragment ion charge PRIDE PRIDE:0000204 product ion charge Charge state PRIDE:PRIDE Fragment ion charge PRIDE A general term for any stable isotope method PRIDE PRIDE:0000205 Heavy stable isotope label A general term for any stable isotope method PRIDE:PRIDE Heavy stable isotope label residue PRIDE PRIDE:0000206 Heavy stable isotope label residue Heavy stable isotope label residue PRIDE:PRIDE Light stable isotope label PRIDE PRIDE:0000207 Light stable isotope label Light stable isotope label PRIDE:PRIDE The precise amino acid that has been modified PRIDE PRIDE:0000208 Light stable isotope label residue The precise amino acid that has been modified PRIDE:PRIDE Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates PRIDE PRIDE:0000209 Peptide pair id Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates PRIDE:PRIDE Ratio of peptide pair the sequence/sample is the numerator in the ratio PRIDE PRIDE:0000210 Stable isotope ratio Ratio of peptide pair the sequence/sample is the numerator in the ratio PRIDE:PRIDE This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample PRIDE PRIDE:0000211 Quantitative sample reference This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample PRIDE:PRIDE Expect value as defined for the Mascot search algorithm PRIDE PRIDE:0000212 Mascot expect value Expect value as defined for the Mascot search algorithm PRIDE:PRIDE The Inspect search algorithm PRIDE PRIDE:0000213 Inspect The Inspect search algorithm PRIDE:PRIDE Quality score of a match PRIDE PRIDE:0000214 Inspect MQScore Quality score of a match PRIDE:PRIDE Probability that the top match is correct PRIDE PRIDE:0000215 Inspect p-value Probability that the top match is correct PRIDE:PRIDE ProteomExchange accession number of the project where the PRIDE experiment is included PRIDE PRIDE:0000216 ProteomExchange project accession number ProteomExchange accession number of the project where the PRIDE experiment is included PRIDE:PRIDE Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included PRIDE PRIDE:0000217 ProteomExchange project hash Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included PRIDE:PRIDE Original format of the file containing MS data PRIDE PRIDE:0000218 Original MS data file format Original format of the file containing MS data PRIDE:PRIDE Date when the search was performed PRIDE PRIDE:0000219 Date of search Date when the search was performed PRIDE:PRIDE M/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge PRIDE PRIDE:0000220 Calculated Mass To Charge Ratio M/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge PRIDE:PRIDE Parent retention time error in minutes PRIDE PRIDE:0000221 parent ion retention time error Parent retention time error in minutes PRIDE:PRIDE X ion type x fragment ion PRIDE PRIDE:0000227 x ion X ion type PRIDE:PRIDE x fragment ion PRIDE X ion type with the neutral loss of a molecule water x fragment ion -H2O PRIDE PRIDE:0000228 x ion -H2O X ion type with the neutral loss of a molecule water PRIDE:PRIDE x fragment ion -H2O PRIDE X ion type with the neutral loss of an ammonia group x fragment ion -NH3 PRIDE PRIDE:0000229 x ion -NH3 X ion type with the neutral loss of an ammonia group PRIDE:PRIDE x fragment ion -NH3 PRIDE Z ion type z fragment ion PRIDE PRIDE:0000230 z ion Z ion type PRIDE:PRIDE z fragment ion PRIDE Z ion type with the neutral loss of a molecule water z fragment ion -H2O PRIDE PRIDE:0000231 z ion -H2O Z ion type with the neutral loss of a molecule water PRIDE:PRIDE z fragment ion -H2O PRIDE Z ion type with the neutral loss of an ammonia group z fragment ion -NH3 PRIDE PRIDE:0000232 z ion -NH3 Z ion type with the neutral loss of an ammonia group PRIDE:PRIDE z fragment ion -NH3 PRIDE A ion type a fragment ion PRIDE PRIDE:0000233 a ion A ion type PRIDE:PRIDE a fragment ion PRIDE A ion type with the neutral loss of a molecule water a fragment ion -H2O PRIDE PRIDE:0000234 a ion -H2O A ion type with the neutral loss of a molecule water PRIDE:PRIDE a fragment ion -H2O PRIDE A ion type with the neutral loss of an ammonia group A fragment ion -NH3 PRIDE PRIDE:0000235 a ion -NH3 A ion type with the neutral loss of an ammonia group PRIDE:PRIDE A fragment ion -NH3 PRIDE C ion type c fragment ion PRIDE PRIDE:0000236 c ion C ion type PRIDE:PRIDE c fragment ion PRIDE C ion type with the neutral loss of a molecule water c fragment ion -H2O PRIDE PRIDE:0000237 c ion -H2O C ion type with the neutral loss of a molecule water PRIDE:PRIDE c fragment ion -H2O PRIDE C ion type with the neutral loss of an ammonia group c fragment ion -NH3 PRIDE PRIDE:0000238 c ion -NH3 C ion type with the neutral loss of an ammonia group PRIDE:PRIDE c fragment ion -NH3 PRIDE Immonium ion type PRIDE PRIDE:0000239 immonium ion Immonium ion type PRIDE:PRIDE Immonium ion type for alanine PRIDE PRIDE:0000240 immonium A Immonium ion type for alanine PRIDE:PRIDE Immonium ion type for cysteine PRIDE PRIDE:0000241 immonium C Immonium ion type for cysteine PRIDE:PRIDE Immonium ion type for aspartic acid PRIDE PRIDE:0000242 immonium D Immonium ion type for aspartic acid PRIDE:PRIDE Immonium ion type for glutamic acid PRIDE PRIDE:0000243 immonium E Immonium ion type for glutamic acid PRIDE:PRIDE Immonium ion type for phenylalanine PRIDE PRIDE:0000244 immonium F Immonium ion type for phenylalanine PRIDE:PRIDE Immonium ion type for glycine PRIDE PRIDE:0000245 immonium G Immonium ion type for glycine PRIDE:PRIDE Immonium ion type for histidine PRIDE PRIDE:0000246 immonium H Immonium ion type for histidine PRIDE:PRIDE Immonium ion type for isoleucine PRIDE PRIDE:0000247 immonium I Immonium ion type for isoleucine PRIDE:PRIDE Immonium ion type for lysine PRIDE PRIDE:0000248 immonium K Immonium ion type for lysine PRIDE:PRIDE Immonium ion type for leucine PRIDE PRIDE:0000249 immonium L Immonium ion type for leucine PRIDE:PRIDE Immonium ion type for methionine PRIDE PRIDE:0000250 immonium M Immonium ion type for methionine PRIDE:PRIDE Immonium ion type for asparagine PRIDE PRIDE:0000251 immonium N Immonium ion type for asparagine PRIDE:PRIDE Immonium ion type for proline PRIDE PRIDE:0000252 immonium P Immonium ion type for proline PRIDE:PRIDE Immonium ion type for glutamine PRIDE PRIDE:0000253 immonium Q Immonium ion type for glutamine PRIDE:PRIDE Immonium ion type for arginine PRIDE PRIDE:0000254 immonium R Immonium ion type for arginine PRIDE:PRIDE Immonium ion type for serine PRIDE PRIDE:0000255 immonium S Immonium ion type for serine PRIDE:PRIDE Immonium ion type for threnine PRIDE PRIDE:0000256 immonium T Immonium ion type for threnine PRIDE:PRIDE Immonium ion type for valine PRIDE PRIDE:0000257 immonium V Immonium ion type for valine PRIDE:PRIDE Immonium ion type for tryptophan PRIDE PRIDE:0000258 immonium W Immonium ion type for tryptophan PRIDE:PRIDE Immonium ion type for tyrosine PRIDE PRIDE:0000259 immonium Y Immonium ion type for tyrosine PRIDE:PRIDE Precursor ion type Parent ion type PRIDE PRIDE:0000260 precursor ion type Precursor ion type PRIDE:PRIDE Parent ion type PRIDE Precursor ion type with the neutral loss of a molecule water Parent ion -H2O PRIDE PRIDE:0000261 precursor ion -H2O Precursor ion type with the neutral loss of a molecule water PRIDE:PRIDE Parent ion -H2O PRIDE Precursor ion type with the neutral loss of an ammonia group Parent ion -NH3 PRIDE PRIDE:0000262 precursor ion -NH3 Precursor ion type with the neutral loss of an ammonia group PRIDE:PRIDE Parent ion -NH3 PRIDE Precursor ion Parent ion PRIDE PRIDE:0000263 precursor ion Precursor ion PRIDE:PRIDE Parent ion PRIDE The name of the sample labelled with iTRAQ reagent 113 PRIDE PRIDE:0000264 iTRAQ reagent 113 The name of the sample labelled with iTRAQ reagent 113 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 118 PRIDE PRIDE:0000265 iTRAQ reagent 118 The name of the sample labelled with iTRAQ reagent 118 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 119 PRIDE PRIDE:0000266 iTRAQ reagent 119 The name of the sample labelled with iTRAQ reagent 119 PRIDE:PRIDE The name of the sample labelled with iTRAQ reagent 121 PRIDE PRIDE:0000267 iTRAQ reagent 121 The name of the sample labelled with iTRAQ reagent 121 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 113 PRIDE PRIDE:0000268 iTRAQ intensity 113 The intensity of the sample labelled with iTRAQ reagent 113 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 118 PRIDE PRIDE:0000269 iTRAQ intensity 118 The intensity of the sample labelled with iTRAQ reagent 118 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 119 PRIDE PRIDE:0000270 iTRAQ intensity 119 The intensity of the sample labelled with iTRAQ reagent 119 PRIDE:PRIDE The intensity of the sample labelled with iTRAQ reagent 121 PRIDE PRIDE:0000271 iTRAQ intensity 121 The intensity of the sample labelled with iTRAQ reagent 121 PRIDE:PRIDE Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page PRIDE PRIDE:0000272 Project secondary name Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page PRIDE:PRIDE 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 PRIDE PRIDE:0000273 SloMo score threshold for valid modification location 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000274 MaxQuant percentage 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000275 SloMo score 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 PRIDE:PRIDE It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide PRIDE PRIDE:0000276 MaxQuant percentage It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide PRIDE:PRIDE A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified PRIDE PRIDE:0000277 Valid location A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified PRIDE:PRIDE 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 PRIDE PRIDE:0000278 Processing method additional parameter 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 PRIDE:PRIDE Enzyme that is selected as a parameter of the search engine PRIDE PRIDE:0000279 In silico enzyme digestion Enzyme that is selected as a parameter of the search engine PRIDE:PRIDE Z ion type with one extra proton zH fragment ion PRIDE PRIDE:0000280 zH ion Z ion type with one extra proton PRIDE:PRIDE zH fragment ion PRIDE Z ion type with two extra protons zHH fragment ion PRIDE PRIDE:0000281 zHH ion Z ion type with two extra protons PRIDE:PRIDE zHH fragment ion PRIDE Fixed type of post-translational modification PRIDE PRIDE:0000282 Fixed modification Fixed type of post-translational modification PRIDE:PRIDE Variable type of post-translational modification PRIDE PRIDE:0000283 Variable modification Variable type of post-translational modification PRIDE:PRIDE 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 PRIDE PRIDE:0000284 Sf 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 PRIDE:PRIDE The name of the sample labelled with TMT reagent 126 PRIDE PRIDE:0000285 TMT reagent 126 The name of the sample labelled with TMT reagent 126 PRIDE:PRIDE The name of the sample labelled with TMT reagent 127 PRIDE PRIDE:0000286 TMT reagent 127 The name of the sample labelled with TMT reagent 127 PRIDE:PRIDE The name of the sample labelled with TMT reagent 128 PRIDE PRIDE:0000287 TMT reagent 128 The name of the sample labelled with TMT reagent 128 PRIDE:PRIDE The name of the sample labelled with TMT reagent 129 PRIDE PRIDE:0000288 TMT reagent 129 The name of the sample labelled with TMT reagent 129 PRIDE:PRIDE The name of the sample labelled with TMT reagent 130 PRIDE PRIDE:0000289 TMT reagent 130 The name of the sample labelled with TMT reagent 130 PRIDE:PRIDE The name of the sample labelled with TMT reagent 131 PRIDE PRIDE:0000290 TMT reagent 131 The name of the sample labelled with TMT reagent 131 PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS] PRIDE PRIDE:0000291 TMT intensity 126 The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS] PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS] PRIDE PRIDE:0000292 TMT intensity 127 The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS] PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS] PRIDE PRIDE:0000293 TMT intensity 128 The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS] PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS] PRIDE PRIDE:0000294 TMT intensity 129 The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS] PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS] PRIDE PRIDE:0000295 TMT intensity 130 The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS] PRIDE:PRIDE The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS] PRIDE PRIDE:0000296 TMT intensity 131 The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS] PRIDE:PRIDE Name of the gene that has been identified (if a nucleotide database was used to perform the search) PRIDE PRIDE:0000297 Gene name Name of the gene that has been identified (if a nucleotide database was used to perform the search) PRIDE:PRIDE Position of the modification in the protein sequence PRIDE PRIDE:0000298 Modification Position in Protein Sequence Position of the modification in the protein sequence PRIDE:PRIDE The original submitted protein accession for this identification. This might have been curated as part of the submission process PRIDE PRIDE:0000299 Submitted Protein Accession The original submitted protein accession for this identification. This might have been curated as part of the submission process PRIDE:PRIDE The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication PRIDE PRIDE:0000300 Gel spot identifier The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication PRIDE:PRIDE 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) PRIDE PRIDE:0000301 Non-significant protein identification 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) PRIDE:PRIDE 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) PRIDE PRIDE:0000302 Non-significant peptide identification 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) PRIDE:PRIDE Indicates that this protein identification comes from the used decoy database PRIDE PRIDE:0000303 Decoy hit Indicates that this protein identification comes from the used decoy database PRIDE:PRIDE The gel's identifier. This identifier should resemble the one used in, for example, the associated publication PRIDE PRIDE:0000304 Gel identifier The gel's identifier. This identifier should resemble the one used in, for example, the associated publication PRIDE:PRIDE Defines a gel-based proteomics experiment PRIDE PRIDE:0000305 Gel-based experiment Defines a gel-based proteomics experiment PRIDE:PRIDE It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses PRIDE PRIDE:0000306 Imported from NCBI Peptidome It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses PRIDE:PRIDE Defines various quantification methods PRIDE PRIDE:0000307 Quantification method Defines various quantification methods PRIDE:PRIDE Describes gel-based quantification methods PRIDE PRIDE:0000308 Gel-based quantification method Describes gel-based quantification methods PRIDE:PRIDE Describes gel-free quantification methods PRIDE PRIDE:0000309 Gel-free quantification method Describes gel-free quantification methods PRIDE:PRIDE Describes quantification techniques using isotope labeling PRIDE PRIDE:0000310 Isotope labeling Describes quantification techniques using isotope labeling PRIDE:PRIDE Describes quantification techniques based on selected / multiple reaction monitoring PRIDE PRIDE:0000311 Selected Reaction Monitoring Describes quantification techniques based on selected / multiple reaction monitoring PRIDE:PRIDE Describes label free quantification techniques PRIDE PRIDE:0000312 Label free Describes label free quantification techniques PRIDE:PRIDE Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level PRIDE PRIDE:0000313 iTRAQ Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level PRIDE:PRIDE Tandem Mass Tag is a MS2 based isotope labeling quantification technique Tandem Mass Tag PRIDE PRIDE:0000314 TMT Tandem Mass Tag is a MS2 based isotope labeling quantification technique PRIDE:PRIDE Tandem Mass Tag PRIDE 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 PRIDE PRIDE:0000315 SILAC Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification PRIDE:PRIDE Stable isotope labeling with amino acids in cell culture PRIDE Describes isotope labeling quantification techniques detectable at MS1 level PRIDE PRIDE:0000316 MS1 based isotope labeling Describes isotope labeling quantification techniques detectable at MS1 level PRIDE:PRIDE Describes isotope labeling quantification techniques detectable at MS2 level PRIDE PRIDE:0000317 MS2 based isotope labeling Describes isotope labeling quantification techniques detectable at MS2 level PRIDE:PRIDE The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen PRIDE PRIDE:0000318 18O The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen PRIDE:PRIDE Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements Isotope-Coded Affinity Tags PRIDE PRIDE:0000319 ICAT Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements PRIDE:PRIDE Isotope-Coded Affinity Tags PRIDE AQUA is an isotope labeling based quantification technique that uses known peptides PRIDE PRIDE:0000320 AQUA AQUA is an isotope labeling based quantification technique that uses known peptides PRIDE:PRIDE Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses Isotope-coded protein label PRIDE PRIDE:0000321 ICPL Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses PRIDE:PRIDE Isotope-coded protein label PRIDE 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 PRIDE PRIDE:0000322 emPAI 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 PRIDE:PRIDE Exponentially Modified Protein Abundance Index PRIDE The Total Ion Current (TIC) can be measured or calculated in order to target specific ions Total Ion Current PRIDE PRIDE:0000323 TIC The Total Ion Current (TIC) can be measured or calculated in order to target specific ions PRIDE:PRIDE Total Ion Current PRIDE A reagent used for quantification PRIDE PRIDE:0000324 Quantification reagent A reagent used for quantification PRIDE:PRIDE The heavy label used in SILAC experiments PRIDE PRIDE:0000325 SILAC heavy The heavy label used in SILAC experiments PRIDE:PRIDE The light reagent used in SILAC experiments PRIDE PRIDE:0000326 SILAC light The light reagent used in SILAC experiments PRIDE:PRIDE The medium weight reagent used in SILAC experiments PRIDE PRIDE:0000327 SILAC medium The medium weight reagent used in SILAC experiments PRIDE:PRIDE Reagent used in SILAC labeling PRIDE PRIDE:0000328 SILAC reagent Reagent used in SILAC labeling PRIDE:PRIDE Reagent used in iTRAQ experiments PRIDE PRIDE:0000329 iTRAQ reagent Reagent used in iTRAQ experiments PRIDE:PRIDE 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 PRIDE PRIDE:0000330 Arbitrary quantification unit 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 PRIDE:PRIDE Quantification values reported as arbitrary counts (most often ion counts) PRIDE PRIDE:0000331 Counts Quantification values reported as arbitrary counts (most often ion counts) PRIDE:PRIDE Reagent used in TMT experiments PRIDE PRIDE:0000337 TMT reagent Reagent used in TMT experiments PRIDE:PRIDE Reagent used in ICAT experiments PRIDE PRIDE:0000344 ICAT reagent Reagent used in ICAT experiments PRIDE:PRIDE The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents PRIDE PRIDE:0000345 ICAT light reagent The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents PRIDE:PRIDE The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling PRIDE PRIDE:0000346 ICAT heavy reagent The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling PRIDE:PRIDE Reagent used in ICPL experiments PRIDE PRIDE:0000347 ICPL reagent Reagent used in ICPL experiments PRIDE:PRIDE 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 PRIDE PRIDE:0000348 ICPL 0 reagent 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000349 ICPL 4 reagent 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 PRIDE:PRIDE The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group PRIDE PRIDE:0000350 ICPL 6 reagent The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group PRIDE:PRIDE The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group PRIDE PRIDE:0000351 ICPL 10 reagent The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group PRIDE:PRIDE Parameters to report quantification values PRIDE PRIDE:0000352 Quantification value Parameters to report quantification values PRIDE:PRIDE Parameters describing quantification values for multiplexed samples PRIDE PRIDE:0000353 Multiplexed quantification value Parameters describing quantification values for multiplexed samples PRIDE:PRIDE Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000354 Intensity subsample 1 Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000355 Intensity subsample 2 Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000356 Intensity subsample 3 Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000357 Intensity subsample 4 Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000358 Intensity subsample 5 Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000359 Intensity subsample 6 Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000360 Intensity subsample 7 Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE PRIDE:0000361 Intensity subsample 8 Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest PRIDE:PRIDE Values from other quantification techniques PRIDE PRIDE:0000362 Other quantification value Values from other quantification techniques PRIDE:PRIDE The emPAI for the protein PRIDE PRIDE:0000363 emPAI value The emPAI for the protein PRIDE:PRIDE The Total Ion Count for the given entity PRIDE PRIDE:0000364 TIC value The Total Ion Count for the given entity PRIDE:PRIDE Describes multiples subsamples PRIDE PRIDE:0000365 Multiplexed sample description Describes multiples subsamples PRIDE:PRIDE Identifies samples that are made up of multiplexed subsamples PRIDE PRIDE:0000366 Contains multiple subsamples Identifies samples that are made up of multiplexed subsamples PRIDE:PRIDE Quantification related parameter PRIDE PRIDE:0000391 Quantification parameter Quantification related parameter PRIDE:PRIDE Unit used to report quantification results PRIDE PRIDE:0000392 Quantification unit Unit used to report quantification results PRIDE:PRIDE Unit to report relative quantification results PRIDE PRIDE:0000393 Relative quantification unit Unit to report relative quantification results PRIDE:PRIDE Unit used to describe absolute quantification results PRIDE PRIDE:0000394 Absolute quantification unit Unit used to describe absolute quantification results PRIDE:PRIDE Quantification results represent ratios PRIDE PRIDE:0000395 Ratio Quantification results represent ratios PRIDE:PRIDE Quantification results are reported as copies per cell PRIDE PRIDE:0000396 Copies per cell Quantification results are reported as copies per cell PRIDE:PRIDE One dataset is a reanalysis of previously published data PRIDE PRIDE:0000397 Data derived from previous dataset One dataset is a reanalysis of previously published data PRIDE:PRIDE No post-translational-modifications are been included in the identified peptides of one dataset PRIDE PRIDE:0000398 No PTMs are included in the dataset No post-translational-modifications are been included in the identified peptides of one dataset PRIDE:PRIDE A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet PRIDE PRIDE:0000399 Accepted manuscript A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet PRIDE:PRIDE 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 value-type:xsd:string PRIDE PRIDE:0000400 Reference 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 PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term This means that the experimental information available has been improved, for instance precursor charges were added PRIDE PRIDE:0000401 Experimental information has been refined since this experiment was originally made publicly available This means that the experimental information available has been improved, for instance precursor charges were added PRIDE:PRIDE A dataset is not a reanalysis of previously published data PRIDE PRIDE:0000402 Original data A dataset is not a reanalysis of previously published data PRIDE:PRIDE URI of one external file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000403 Associated file URI URI of one external file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of a raw data file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000404 Associated raw file URI URI of a raw data file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission) PRIDE PRIDE:0000405 Submit PRIDE Experiment to IntAct Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission) PRIDE:PRIDE URI associated to one PX submission in ProteomeCentral value-type:xsd:string PRIDE PRIDE:0000406 ProteomeCentral dataset URI URI associated to one PX submission in ProteomeCentral PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one file labeled as 'Result', associated to one PX submission value-type:xsd:string PRIDE PRIDE:0000407 Result file URI URI of one file labeled as 'Result', associated to one PX submission PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one search engine output file associated to one PX submission value-type:xsd:string PRIDE PRIDE:0000408 Search engine output file URI URI of one search engine output file associated to one PX submission PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one of one search engine output file associated to one PX submission value-type:xsd:string PRIDE PRIDE:0000409 Peak list file URI URI of one of one search engine output file associated to one PX submission PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one file labeled as 'Other', associated to one PX submission value-type:xsd:string PRIDE PRIDE:0000410 'Other' type file URI URI of one file labeled as 'Other', associated to one PX submission PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term FTP location of one entire PX data set value-type:xsd:string PRIDE PRIDE:0000411 Dataset FTP location FTP location of one entire PX data set PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term A dataset which does not have an associated published manuscript PRIDE PRIDE:0000412 Dataset with no associated published manuscript A dataset which does not have an associated published manuscript PRIDE:PRIDE 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 value-type:xsd:string PRIDE PRIDE:0000413 Instrument name 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 PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term Dataset has been peer-reviewed somehow PRIDE PRIDE:0000414 Peer-reviewed dataset Dataset has been peer-reviewed somehow PRIDE:PRIDE Dataset that has not been peer-reviewed by any means PRIDE PRIDE:0000415 Non peer-reviewed dataset Dataset that has not been peer-reviewed by any means PRIDE:PRIDE The PX dataset is supported by and is available through the submission repository PRIDE PRIDE:0000416 Supported dataset by repository The PX dataset is supported by and is available through the submission repository PRIDE:PRIDE The PX dataset is not fully supported by the submission repository PRIDE PRIDE:0000417 Unsupported dataset by repository The PX dataset is not fully supported by the submission repository PRIDE:PRIDE 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 PRIDE PRIDE:0000418 Other member of protein ambiguity group 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 PRIDE:PRIDE B ion type with a neutral loss of a phosphate molecule B fragment ion -H3PO4 PRIDE PRIDE:0000419 b ion -H3PO4 B ion type with a neutral loss of a phosphate molecule PRIDE:PRIDE B fragment ion -H3PO4 PRIDE B ion type with a neutral loss of 2 phosphate molecules B fragment ion -2H3PO4 PRIDE PRIDE:0000420 b ion -2H3PO4 B ion type with a neutral loss of 2 phosphate molecules PRIDE:PRIDE B fragment ion -2H3PO4 PRIDE B ion type with a neutral loss of 3 phosphate molecules B fragment ion -3H3PO4 PRIDE PRIDE:0000421 b ion -3H3PO4 B ion type with a neutral loss of 3 phosphate molecules PRIDE:PRIDE B fragment ion -3H3PO4 PRIDE Y ion type with a neutral loss of a phosphate molecule y fragment ion -H3PO4 PRIDE PRIDE:0000422 y ion -H3PO4 Y ion type with a neutral loss of a phosphate molecule PRIDE:PRIDE y fragment ion -H3PO4 PRIDE Y ion type with a neutral loss of 2 phosphate molecules y fragment ion -2H3PO4 PRIDE PRIDE:0000423 y ion -2H3PO4 Y ion type with a neutral loss of 2 phosphate molecules PRIDE:PRIDE y fragment ion -2H3PO4 PRIDE Y ion type with a neutral loss of 3 phosphate molecules y fragment ion -3H3PO4 PRIDE PRIDE:0000424 y ion -3H3PO4 Y ion type with a neutral loss of 3 phosphate molecules PRIDE:PRIDE y fragment ion -3H3PO4 PRIDE A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples PRIDE PRIDE:0000425 MS1 intensity based label-free quantification method A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples PRIDE:PRIDE The basic mass spectrometry strategy used in the experiment PRIDE PRIDE:0000426 Mass spectrometry proteomics experimental strategy The basic mass spectrometry strategy used in the experiment PRIDE:PRIDE A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics) PRIDE PRIDE:0000427 Top-down proteomics A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics) PRIDE:PRIDE Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer PRIDE PRIDE:0000428 Bottom-up proteomics Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer PRIDE:PRIDE 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 PRIDE PRIDE:0000429 MS/MS shotgun proteomics 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 PRIDE:PRIDE Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction PRIDE PRIDE:0000430 Chemical cross-linking coupled with mass spectrometry proteomics Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction PRIDE:PRIDE Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction PRIDE PRIDE:0000431 Affinity purification 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 PRIDE:PRIDE A dataset which has an associated manuscript pending for publication PRIDE PRIDE:0000432 Dataset with its publication pending A dataset which has an associated manuscript pending for publication PRIDE:PRIDE Labeled reagents used for quantification PRIDE PRIDE:0000433 Reagents used in Labeled Methods Labeled reagents used for quantification PRIDE:PRIDE An unlabeled sample used for quantification PRIDE PRIDE:0000434 Unlabeled sample An unlabeled sample used for quantification PRIDE:PRIDE Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 PRIDE PRIDE:0000435 Peptide counting Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 PRIDE:PRIDE Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 PRIDE PRIDE:0000436 Spectrum counting Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 PRIDE:PRIDE Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 PRIDE PRIDE:0000437 PAI Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 PRIDE:PRIDE Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 PRIDE PRIDE:0000438 Spectrum count/molecular weight Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 PRIDE:PRIDE The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 PRIDE PRIDE:0000439 SAF The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 PRIDE:PRIDE Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 PRIDE PRIDE:0000440 NSAF Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 PRIDE:PRIDE Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 PRIDE PRIDE:0000441 APEX - Absolute Protein Expression Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 PRIDE:PRIDE Tissue not applicable to dataset PRIDE PRIDE:0000442 Tissue not applicable to dataset Tissue not applicable to dataset PRIDE:PRIDE The NCBI FTP location of the original Sample - Experiment level Peptidome submission data PRIDE PRIDE:0000443 Original NCBI Peptidome submission files The NCBI FTP location of the original Sample - Experiment level Peptidome submission data PRIDE:PRIDE Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system) PRIDE PRIDE:0000444 PRIDE experiment accession Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system) PRIDE:PRIDE 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) PRIDE PRIDE:0000445 PRIDE Cluster score 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) PRIDE:PRIDE Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243 PRIDE PRIDE:0000446 PRIDE peptide score Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243 PRIDE:PRIDE 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 PRIDE PRIDE:0000447 SWATH MS 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 PRIDE:PRIDE 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 value-type:xsd:string PRIDE PRIDE:0000448 Additional associated raw file URI 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 PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one gel image file associated to one PX submission value-type:xsd:string PRIDE PRIDE:0000449 Gel image file URI URI of one gel image file associated to one PX submission PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term 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 PRIDE PRIDE:0000450 Data-independent acquisition 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000451 MSE 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000452 HDMSE 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000453 PAcIFIC 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000454 All-ion fragmentation 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 PRIDE:PRIDE Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction PRIDE PRIDE:0000455 Protein-protein cross-linking experiment Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction PRIDE:PRIDE Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction PRIDE PRIDE:0000456 Protein-RNA cross-linking experiment Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction PRIDE:PRIDE Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method PRIDE PRIDE:0000457 Experiment Type Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method PRIDE:PRIDE Studying all protein samples of diverse host environments like the human body, soil or sea water Community Proteomics PRIDE Environmental Proteomics PRIDE:0000458 Metaproteomics Studying all protein samples of diverse host environments like the human body, soil or sea water PRIDE:PRIDE Community Proteomics PRIDE Environmental Proteomics PRIDE:PRIDE Investigating both human host proteins and associated microbial proteins at the same time from human samples PRIDE PRIDE:0000459 Human Metaproteomics Investigating both human host proteins and associated microbial proteins at the same time from human samples PRIDE:PRIDE Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies PRIDE PRIDE:0000460 Proteogenomics Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies PRIDE:PRIDE Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples PRIDE PRIDE:0000461 Multi-omics study Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples PRIDE:PRIDE Waters data independent acquisition method PRIDE PRIDE:0000462 SONAR Waters data independent acquisition method PRIDE:PRIDE Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis PRIDE PRIDE:0000463 PRM Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis PRIDE:PRIDE URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000464 Fasta file URI URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000465 Spectral Library file URI URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000466 Quantification result file URI URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission) value-type:xsd:string PRIDE PRIDE:0000467 MS Image file URI URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission) PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI for an Aspera Download Protocol value-type:xsd:string PRIDE PRIDE:0000468 Aspera Protocol URI for an Aspera Download Protocol PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term URI for an FTP Download Protocol PRIDE PRIDE:0000469 FTP Protocol URI for an FTP Download Protocol PRIDE:PRIDE PRIDE File Properties for all type of files PRIDE PRIDE:0000470 File Properties PRIDE File Properties for all type of files PRIDE:PRIDE Properties for MS , Peaks files PRIDE PRIDE:0000471 MS File Properties Properties for MS , Peaks files PRIDE:PRIDE Minimum charge for all precursor in the file PRIDE PRIDE:0000472 MS min charge Minimum charge for all precursor in the file PRIDE:PRIDE Maximum charge for all precursor in the file PRIDE PRIDE:0000473 MS max charge Maximum charge for all precursor in the file PRIDE:PRIDE Minimum retention time in the File PRIDE PRIDE:0000474 MS min RT Minimum retention time in the File PRIDE:PRIDE Maximum retention time in the file PRIDE PRIDE:0000475 MS max RT Maximum retention time in the file PRIDE:PRIDE Minimum precursor mass to charge in the file PRIDE PRIDE:0000476 MS min MZ Minimum precursor mass to charge in the file PRIDE:PRIDE Maximum precursor mass to charge in the file PRIDE PRIDE:0000477 MS max MZ Maximum precursor mass to charge in the file PRIDE:PRIDE Total number of scans in the file PRIDE PRIDE:0000478 Number of scans Total number of scans in the file PRIDE:PRIDE Range of scan number in the ms file PRIDE PRIDE:0000479 MS scan range Range of scan number in the ms file PRIDE:PRIDE Number of MS in the file PRIDE PRIDE:0000480 Number of MS Number of MS in the file PRIDE:PRIDE Number of MS1 spectra PRIDE PRIDE:0000481 Number of MS1 spectra Number of MS1 spectra PRIDE:PRIDE Number of MS2 spectra in the file PRIDE PRIDE:0000482 Number of MS2 spectra Number of MS2 spectra in the file PRIDE:PRIDE Total number of MS3 spectra in the file PRIDE PRIDE:0000483 Number of MS3 spectra Total number of MS3 spectra in the file PRIDE:PRIDE The result analysis parameters is a term to group all the parameters for proteomics data analysis PRIDE PRIDE:0000484 Result analysis parameters The result analysis parameters is a term to group all the parameters for proteomics data analysis PRIDE:PRIDE Result analysis parameters share by multiple search engine and Quantiative tools PRIDE PRIDE:0000485 Global result parameters Result analysis parameters share by multiple search engine and Quantiative tools PRIDE:PRIDE Result analysis parameters specific to a search engine or quantitative tool PRIDE PRIDE:0000486 Tool specific analysis parameters Result analysis parameters specific to a search engine or quantitative tool PRIDE:PRIDE Minimum charge of precursor to be search PRIDE PRIDE:0000487 Min charge Minimum charge of precursor to be search PRIDE:PRIDE Maximum charge of precursor to be search PRIDE PRIDE:0000488 Max charge Maximum charge of precursor to be search PRIDE:PRIDE Min Retention time for precursor to be search PRIDE PRIDE:0000489 Min RT Min Retention time for precursor to be search PRIDE:PRIDE Maximum precursor RT to be search PRIDE PRIDE:0000490 Max RT Maximum precursor RT to be search PRIDE:PRIDE Number of missed cleavages PRIDE PRIDE:0000491 Number of missed cleavages Number of missed cleavages PRIDE:PRIDE Max peptide amino acid length for search PRIDE PRIDE:0000492 Max peptide AA length Max peptide amino acid length for search PRIDE:PRIDE Minimum peptide amino acid length for search PRIDE PRIDE:0000493 Min peptide AA length Minimum peptide amino acid length for search PRIDE:PRIDE Min precursor MZ (mass) for precursor to search PRIDE PRIDE:0000494 Min precursor MZ Min precursor MZ (mass) for precursor to search PRIDE:PRIDE Max precursor MZ (mass) for precursor to search PRIDE PRIDE:0000495 Max precursor MZ Max precursor MZ (mass) for precursor to search PRIDE:PRIDE Min number of peaks in the spectrum to be search PRIDE PRIDE:0000496 Min peak length Min number of peaks in the spectrum to be search PRIDE:PRIDE Use Multi Modification PRIDE PRIDE:0000497 Use Multi Modification Use Multi Modification PRIDE:PRIDE Use Additional Variable Modifications PRIDE PRIDE:0000498 Use Additional Variable Modifications Use Additional Variable Modifications PRIDE:PRIDE Do Mass Filtering PRIDE PRIDE:0000499 Do Mass Filtering Do Mass Filtering PRIDE:PRIDE Intensity Threshold PRIDE PRIDE:0000500 Intensity Threshold Intensity Threshold PRIDE:PRIDE Max Labeled AA PRIDE PRIDE:0000501 Max Labeled AA Max Labeled AA PRIDE:PRIDE Max Number of Modifications (PTMs) PRIDE PRIDE:0000502 Max Number of Modifications (PTMs) Max Number of Modifications (PTMs) PRIDE:PRIDE First Search Precursor Tolerance PRIDE PRIDE:0000503 First Search Precursor Tolerance First Search Precursor Tolerance PRIDE:PRIDE Main Search Precursor Tolerance PRIDE PRIDE:0000504 Main Search Precursor Tolerance Main Search Precursor Tolerance PRIDE:PRIDE Accession or Code of the individual in the sample PRIDE PRIDE:0000505 Individual Accession Accession or Code of the individual in the sample PRIDE:PRIDE Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment PRIDE PRIDE:0000506 Number identified proteins Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment PRIDE:PRIDE Total number of identified peptides in an experiment or assay PRIDE PRIDE:0000507 Number of identified peptides Total number of identified peptides in an experiment or assay PRIDE:PRIDE The total number of peptides identified with post-translational modifications PRIDE PRIDE:0000508 Number of modified peptides The total number of peptides identified with post-translational modifications PRIDE:PRIDE Total number of reported identified Peptide Spectrum matches (PSMs) PRIDE PRIDE:0000509 Number of PSMs Total number of reported identified Peptide Spectrum matches (PSMs) PRIDE:PRIDE The size of the file in MB PRIDE PRIDE:0000510 File size The size of the file in MB PRIDE:PRIDE Pass submitter threshold PRIDE PRIDE:0000511 Pass submitter threshold Pass submitter threshold PRIDE:PRIDE RNA mass spectrometry PRIDE PRIDE:0000512 RNA mass spectrometry RNA mass spectrometry PRIDE:PRIDE Dimethyl Labeling (DML) PRIDE PRIDE:0000513 Dimethyl Labeling Dimethyl Labeling (DML) PRIDE:PRIDE Quantification channel label PRIDE PRIDE:0000514 Label Quantification channel label PRIDE:PRIDE TMT126 PRIDE PRIDE:0000516 TMT126 TMT126 PRIDE:PRIDE TMT127 PRIDE PRIDE:0000517 TMT127 TMT127 PRIDE:PRIDE TMT127C PRIDE PRIDE:0000518 TMT127C TMT127C PRIDE:PRIDE TMT127N PRIDE PRIDE:0000519 TMT127N TMT127N PRIDE:PRIDE TMT128 PRIDE PRIDE:0000520 TMT128 TMT128 PRIDE:PRIDE TMT128C PRIDE PRIDE:0000521 TMT128C TMT128C PRIDE:PRIDE TMT128N PRIDE PRIDE:0000522 TMT128N TMT128N PRIDE:PRIDE TMT129 PRIDE PRIDE:0000523 TMT129 TMT129 PRIDE:PRIDE TMT129C PRIDE PRIDE:0000524 TMT129C TMT129C PRIDE:PRIDE TMT129N PRIDE PRIDE:0000525 TMT129N TMT129N PRIDE:PRIDE TMT130 PRIDE PRIDE:0000526 TMT130 TMT130 PRIDE:PRIDE TMT130C PRIDE PRIDE:0000527 TMT130C TMT130C PRIDE:PRIDE TMT130N PRIDE PRIDE:0000528 TMT130N TMT130N PRIDE:PRIDE TMT131 PRIDE PRIDE:0000529 TMT131 TMT131 PRIDE:PRIDE ITRAQ channel label PRIDE PRIDE:0000530 ITRAQ ITRAQ channel label PRIDE:PRIDE ITRAQ113 channel PRIDE PRIDE:0000531 ITRAQ113 ITRAQ113 channel PRIDE:PRIDE ITRAQ114 channel PRIDE PRIDE:0000532 ITRAQ114 ITRAQ114 channel PRIDE:PRIDE ITRAQ115 channel PRIDE PRIDE:0000533 ITRAQ115 ITRAQ115 channel PRIDE:PRIDE ITRAQ116 channel PRIDE PRIDE:0000534 ITRAQ116 ITRAQ116 channel PRIDE:PRIDE ITRAQ117 channel PRIDE PRIDE:0000535 ITRAQ117 ITRAQ117 channel PRIDE:PRIDE ITRAQ118 channel PRIDE PRIDE:0000536 ITRAQ118 ITRAQ118 channel PRIDE:PRIDE ITRAQ119 channel PRIDE PRIDE:0000537 ITRAQ119 ITRAQ119 channel PRIDE:PRIDE ITRAQ121 channel PRIDE PRIDE:0000538 ITRAQ121 ITRAQ121 channel PRIDE:PRIDE ICAT heavy PRIDE PRIDE:0000541 ICAT heavy ICAT heavy PRIDE:PRIDE ICAT light PRIDE PRIDE:0000542 ICAT light ICAT light PRIDE:PRIDE MS experiments conducted to control the quality of measurements PRIDE PRIDE:0000543 Quality Control MS experiments conducted to control the quality of measurements PRIDE:PRIDE Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings PRIDE PRIDE:0000544 Quality Control Sample Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings PRIDE:PRIDE QC1 sample as described in 10.1371/journal.pone.0189209 PRIDE PRIDE:0000545 QC1 sample QC1 sample as described in 10.1371/journal.pone.0189209 PRIDE:PRIDE QC2 sample as described in 10.1371/journal.pone.0189209 PRIDE PRIDE:0000546 QC2 sample QC2 sample as described in 10.1371/journal.pone.0189209 PRIDE:PRIDE Instrument properties PRIDE PRIDE:0000547 Instrument properties Instrument properties PRIDE:PRIDE MS1 mass analyzer PRIDE PRIDE:0000548 MS1 mass analyzer MS1 mass analyzer PRIDE:PRIDE MS2 mass analyzer PRIDE PRIDE:0000549 MS2 mass analyzer MS2 mass analyzer PRIDE:PRIDE Umbrella term for different types of fractionation methods PRIDE PRIDE:0000550 Fractionation method Umbrella term for different types of fractionation methods PRIDE:PRIDE Umbrella term for different types of separation methods PRIDE PRIDE:0000551 Separation method Umbrella term for different types of separation methods PRIDE:PRIDE Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030) PRIDE PRIDE:0000552 Off-gel electrophoresis Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030) PRIDE:PRIDE 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 PRIDE PRIDE:0000553 Isoelectric focusing 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 PRIDE:PRIDE Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity PRIDE PRIDE:0000554 Hydrophilic interaction chromatography (HILIC) Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity PRIDE:PRIDE 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 PRIDE PRIDE:0000555 ERLIC 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 PRIDE:PRIDE A chromatography method where the separation is caused by differences in ion-exchange affinity PRIDE PRIDE:0000556 Ion-exchange chromatography A chromatography method where the separation is caused by differences in ion-exchange affinity PRIDE:PRIDE A chromatography method where the separation is caused by differences in molecular size PRIDE PRIDE:0000557 Size-exclusion chromatography (SEC) A chromatography method where the separation is caused by differences in molecular size PRIDE:PRIDE A chromatography method with the stationary phase being a strong anion exchanger PRIDE PRIDE:0000558 Strong anion-exchange chromatography (SAX) A chromatography method with the stationary phase being a strong anion exchanger PRIDE:PRIDE A chromatography method with the stationary phase being a weak anion exchanger PRIDE PRIDE:0000559 Weak anion-exchange chromatography (WAX) A chromatography method with the stationary phase being a weak anion exchanger PRIDE:PRIDE A chromatography method with the stationary phase being a weak cation exchanger PRIDE PRIDE:0000560 Weak cation-exchange chromatography (WCX) A chromatography method with the stationary phase being a weak cation exchanger PRIDE:PRIDE A chromatography method with the stationary phase being a strong cation exchanger PRIDE PRIDE:0000561 Strong cation-exchange chromatography (SCX) A chromatography method with the stationary phase being a strong cation exchanger PRIDE:PRIDE Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography PRIDE PRIDE:0000562 Normal-phase liquid chromatography (NP) Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography PRIDE:PRIDE Liquid chromatography where the mobile phase is significantly more polar than the stationary phase PRIDE PRIDE:0000563 Reversed-phase chromatography (RP) Liquid chromatography where the mobile phase is significantly more polar than the stationary phase PRIDE:PRIDE Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase PRIDE PRIDE:0000564 High-pH reversed-phase chromatography (hpHRP) Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase PRIDE:PRIDE Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high http://purl.obolibrary.org/obo/CHMO_0001009 PRIDE PRIDE:0000565 High-performance liquid chromatography Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high PRIDE:PRIDE An electrophoresis method with significantly higher resolution than common isoelectric focusing methods PRIDE PRIDE:0000566 High-resolution isoelectric focusing (HiRIEF) An electrophoresis method with significantly higher resolution than common isoelectric focusing methods PRIDE:PRIDE Gel electrophoresis PRIDE PRIDE:0000567 Gel electrophoresis Gel electrophoresis PRIDE:PRIDE SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel PRIDE PRIDE:0000568 SDS PAGE SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel PRIDE:PRIDE 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) PRIDE PRIDE:0000569 2D PAGE 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) PRIDE:PRIDE A software that perform protein quantification using mass spectrometry data PRIDE PRIDE:0000571 Quantification software A software that perform protein quantification using mass spectrometry data PRIDE:PRIDE 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 PRIDE PRIDE:0000572 OpenMS 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 PRIDE:PRIDE A software that perform peptide/protein identification using mass spectrometry data PRIDE PRIDE:0000573 Identification software A software that perform peptide/protein identification using mass spectrometry data PRIDE:PRIDE MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data PRIDE PRIDE:0000574 MaxQuant MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data PRIDE:PRIDE Threshold at precursor level to compare experimental mass with theoretical mass PRIDE PRIDE:0000575 precursor mass tolerance Threshold at precursor level to compare experimental mass with theoretical mass PRIDE:PRIDE Threshold at fragment level to compare experimental mass with theoretical mass PRIDE PRIDE:0000576 fragment mass tolerance Threshold at fragment level to compare experimental mass with theoretical mass PRIDE:PRIDE URI of one external file associated to the PRIDE experiment on SDRF files definitions PRIDE PRIDE:0000577 file uri URI of one external file associated to the PRIDE experiment on SDRF files definitions PRIDE:PRIDE The bound fraction after a depletion process PRIDE PRIDE:0000578 Bound fraction The bound fraction after a depletion process PRIDE:PRIDE The depleted fraction after a depletion process PRIDE PRIDE:0000579 Depleted fraction The depleted fraction after a depletion process PRIDE:PRIDE TMT131N PRIDE PRIDE:0000580 TMT131N TMT131N PRIDE:PRIDE TMT131C PRIDE PRIDE:0000581 TMT131C TMT131C PRIDE:PRIDE TMT132N PRIDE PRIDE:0000582 TMT132N TMT132N PRIDE:PRIDE TMT132C PRIDE PRIDE:0000583 TMT132C TMT132C PRIDE:PRIDE Experimental design file URI PRIDE PRIDE:0000584 Experimental design file URI Experimental design file URI PRIDE:PRIDE Enrichment of specific post-translational modifications PRIDE PRIDE:0000585 Enrichment Enrichment of specific post-translational modifications PRIDE:PRIDE Enrichment method Enrichment of specific post-translational modifications PRIDE PRIDE:0000586 Enrichment method Enrichment method Enrichment of specific post-translational modifications PRIDE:PRIDE The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides PRIDE PRIDE:0000587 IMAC The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides PRIDE:PRIDE 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 PRIDE PRIDE:0000588 TIO2 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 PRIDE:PRIDE A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy) PRIDE PRIDE:0000589 EThcD A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy) PRIDE:PRIDE Beam-type collision-induced dissociation PRIDE PRIDE:0000590 HCD Beam-type collision-induced dissociation PRIDE:PRIDE Collision-induced dissociation PRIDE PRIDE:0000591 CID Collision-induced dissociation PRIDE:PRIDE ETD with supplemental activation ETcaD PRIDE PRIDE:0000592 ETciD ETD with supplemental activation PRIDE:PRIDE ETcaD PRIDE CID collision energy PRIDE PRIDE:0000593 CID collision energy CID collision energy PRIDE:PRIDE HCD collision energy PRIDE PRIDE:0000594 HCD collision energy HCD collision energy PRIDE:PRIDE EThcD collision energy PRIDE PRIDE:0000595 EThcD collision energy EThcD collision energy PRIDE:PRIDE ETciD collision energy PRIDE PRIDE:0000596 ETciD collision energy ETciD collision energy PRIDE:PRIDE Metabolic label PRIDE PRIDE:0000597 metabolic label Metabolic label PRIDE:PRIDE The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds PRIDE PRIDE:0000598 Alkylation reagent The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds PRIDE:PRIDE The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE PRIDE:0000599 Iodoacetamide (IAA) The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE:PRIDE The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE PRIDE:0000600 Chloroacetamide (ClAA) The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE:PRIDE The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE PRIDE:0000601 Iodoacetic acid (IAC) The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE:PRIDE The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE PRIDE:0000602 Chloroacetic acid (ClAC) The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE:PRIDE 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 PRIDE PRIDE:0000603 Acrylamide (AA) 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000604 4-Vinylpyridine (4-VP) 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000605 Methyl methanethiosulfonate (MMTS) 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 PRIDE:PRIDE The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da PRIDE PRIDE:0000606 N-ethylmaleimide (NEM) The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da PRIDE:PRIDE The chemical reagent that is used to break disulfide bonds in proteins PRIDE PRIDE:0000607 Reduction reagent The chemical reagent that is used to break disulfide bonds in proteins PRIDE:PRIDE The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2 PRIDE PRIDE:0000608 Dithiothreitol (DTT) The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2 PRIDE:PRIDE The reduction agent with chemincal formuls C9H15O6P PRIDE PRIDE:0000609 Tris(2-carboxyethyl)phosphine (TCEP) The reduction agent with chemincal formuls C9H15O6P PRIDE:PRIDE The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS PRIDE PRIDE:0000610 Beta-mercaptoethanol (BME) The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS PRIDE:PRIDE The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4) PRIDE PRIDE:0000611 SILAC light R:12C(6)14N(4) The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4) PRIDE:PRIDE The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6) PRIDE PRIDE:0000612 SILAC light L:12C(6) The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6) PRIDE:PRIDE The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2) PRIDE PRIDE:0000613 SILAC light K:12C(6)14N(2) The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2) PRIDE:PRIDE The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5) PRIDE PRIDE:0000614 SILAC light P:12C(5) The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5) PRIDE:PRIDE The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4) PRIDE PRIDE:0000615 SILAC heavy R:13C(6)15N(4) The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4) PRIDE:PRIDE The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6) PRIDE PRIDE:0000616 SILAC heavy L:13C(6) The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6) PRIDE:PRIDE The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2) PRIDE PRIDE:0000617 SILAC heavy K:13C(6)15N(2) The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2) PRIDE:PRIDE The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4) PRIDE PRIDE:0000618 SILAC medium R:13C(6)14N(4) The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4) PRIDE:PRIDE The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2) PRIDE PRIDE:0000619 SILAC medium K:13C(6)14N(2) The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2) PRIDE:PRIDE Metabolic label 15N PRIDE PRIDE:0000620 15N Metabolic label 15N PRIDE:PRIDE Metabolic label 13C PRIDE PRIDE:0000621 13C Metabolic label 13C PRIDE:PRIDE Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics PRIDE PRIDE:0000623 source name Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics PRIDE:PRIDE Spectra Cluster Maximum Ratio for the cluster PRIDE PRIDE:0000624 SpectraCluster MaxRatio Spectra Cluster Maximum Ratio for the cluster PRIDE:PRIDE NIST Probability Correlation PRIDE PRIDE:0000625 NIST ProbCorr NIST Probability Correlation PRIDE:PRIDE NIST best dot product PRIDE PRIDE:0000626 NIST Dotbest NIST best dot product PRIDE:PRIDE Data-dependent acquisition PRIDE PRIDE:0000627 Data-dependent acquisition Data-dependent acquisition PRIDE:PRIDE Parallel Reaction Monitoring (PRM) PRIDE PRIDE:0000629 Parallel reaction monitoring Parallel Reaction Monitoring (PRM) PRIDE:PRIDE Selected reaction monitoring (SRM) PRIDE PRIDE:0000630 Selected reaction monitoring Selected reaction monitoring (SRM) PRIDE:PRIDE Mass spectrometry imaging PRIDE PRIDE:0000631 Mass spectrometry imaging Mass spectrometry imaging PRIDE:PRIDE TMT133N PRIDE PRIDE:0000632 TMT133N TMT133N PRIDE:PRIDE TMT133C PRIDE PRIDE:0000633 TMT133C TMT133C PRIDE:PRIDE TMT134 PRIDE PRIDE:0000634 TMT134 TMT134 PRIDE:PRIDE The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes PRIDE PRIDE:0000635 Affinity proteomics The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes PRIDE:PRIDE 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 PRIDE PRIDE:0000636 SomaScan affinity proteomics 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000637 Olink affinity proteomics 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 PRIDE:PRIDE Instrument model PRIDE PRIDE:0000638 Instrument model Instrument model PRIDE:PRIDE Somalogic instrument model PRIDE PRIDE:0000639 Somalogic instrument model Somalogic instrument model PRIDE:PRIDE SomaScan assay v4.0 PRIDE PRIDE:0000640 SomaScan assay v4.0 SomaScan assay v4.0 PRIDE:PRIDE SomaScan assay v4.1 PRIDE PRIDE:0000641 SomaScan assay v4.1 SomaScan assay v4.1 PRIDE:PRIDE TMT134C PRIDE PRIDE:0000642 TMT134C TMT134C PRIDE:PRIDE TMT134N PRIDE PRIDE:0000643 TMT134N TMT134N PRIDE:PRIDE Fragmentation method used for dissociation or fragmentation for MS2 PRIDE PRIDE:0000644 MS2 dissociation method Fragmentation method used for dissociation or fragmentation for MS2 PRIDE:PRIDE Fragmentation method used for dissociation or fragmentation for MS3 PRIDE PRIDE:0000645 MS3 dissociation method Fragmentation method used for dissociation or fragmentation for MS3 PRIDE:PRIDE MS3 mass analyzer PRIDE PRIDE:0000646 MS3 mass analyzer MS3 mass analyzer PRIDE:PRIDE Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome PRIDE PRIDE:0000649 Immunopeptidomics Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome PRIDE:PRIDE Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 PRIDE PRIDE:0000650 diaPASEF Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 PRIDE:PRIDE Absolute quantification precisely measures the concentration of a specific analyte in a sample PRIDE PRIDE:0000651 Absolute quantification Absolute quantification precisely measures the concentration of a specific analyte in a sample PRIDE:PRIDE Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples PRIDE PRIDE:0000652 Relative quantification Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples PRIDE:PRIDE Normalized Protein eXpression PRIDE PRIDE:0000653 NPX Normalized Protein eXpression PRIDE:PRIDE Olink instrument model PRIDE PRIDE:0000654 Olink instrument model Olink instrument model PRIDE:PRIDE Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology PRIDE PRIDE:0000655 Olink Target 96 Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology PRIDE:PRIDE Olink Explore 1536 PRIDE PRIDE:0000656 Olink Explore 1536 Olink Explore 1536 PRIDE:PRIDE Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies PRIDE PRIDE:0000657 Olink Explore 3072/384 Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies PRIDE:PRIDE Olink Explore 384 PRIDE PRIDE:0000658 Olink Explore 384 Olink Explore 384 PRIDE:PRIDE Proteomics data acquisition method PRIDE PRIDE:0000659 Proteomics data acquisition method Proteomics data acquisition method PRIDE:PRIDE Ion Mobility Separation PRIDE PRIDE:0000660 Ion Mobility Separation Ion Mobility Separation PRIDE:PRIDE Differential mobility Separation PRIDE PRIDE:0000661 Differential mobility Separation Differential mobility Separation PRIDE:PRIDE SelexION differential mobility separation device PRIDE PRIDE:0000662 SelexION Separation Method SelexION differential mobility separation device PRIDE:PRIDE The technology type or platform used to perform the study PRIDE PRIDE:0000663 technology type The technology type or platform used to perform the study EFO:EFO_0005521 An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry PRIDE PRIDE:0000664 proteomic profiling by mass spectrometry An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry EFO:EFO_0002766 Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications PRIDE PRIDE:0000665 Glycoproteomics Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications PRIDE:PRIDE TMT 6-plex labeling kit has 6 channels PRIDE PRIDE:0000666 TMT6PLEX TMT 6-plex labeling kit has 6 channels PRIDE:PRIDE TMT 10-plex labeling kit has 10 channels PRIDE PRIDE:0000667 TMT10PLEX TMT 10-plex labeling kit has 10 channels PRIDE:PRIDE TMT 16-plex labeling kit has 16 channels PRIDE PRIDE:0000668 TMT16PLEX TMT 16-plex labeling kit has 16 channels PRIDE:PRIDE TMT 18-plex labeling kit has 18 channels PRIDE PRIDE:0000669 TMT18PLEX TMT 18-plex labeling kit has 18 channels PRIDE:PRIDE TMT135 PRIDE PRIDE:0000670 TMT135 TMT135 PRIDE:PRIDE Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology PRIDE PRIDE:0000671 Olink Explore Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology PRIDE:PRIDE Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology PRIDE PRIDE:0000672 Olink Target Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology PRIDE:PRIDE 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 PRIDE PRIDE:0000673 Olink Explore HT 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 PRIDE:PRIDE A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome. PRIDE PRIDE:0000674 human gut A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome. PRIDE:PRIDE 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 sample name PRIDE PRIDE:0000675 sample name 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 PRIDE:PRIDE Name of the project within which the sequencing was organized. MIXS:0000092 project name PRIDE PRIDE:0000676 project name Name of the project within which the sequencing was organized. MIXS:0000092 PRIDE:PRIDE History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280 PRIDE PRIDE:0000677 gastrointestinal tract disorder History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280 PRIDE:PRIDE History of liver disorders; can include multiple disorders. MIXS:0000282 PRIDE PRIDE:0000678 liver disorder History of liver disorders; can include multiple disorders. MIXS:0000282 PRIDE:PRIDE Specification of special diet; can include multiple special diets. MIXS:0000905 PRIDE PRIDE:0000679 special diet Specification of special diet; can include multiple special diets. MIXS:0000905 PRIDE:PRIDE A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861 PRIDE PRIDE:0000680 host subject id A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861 PRIDE:PRIDE 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 host age slot PRIDE PRIDE:0000681 host age 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 PRIDE:PRIDE List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031 host disease slot PRIDE PRIDE:0000682 host disease status List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031 PRIDE:PRIDE Can include multiple medication codes. MIXS:0000884 PRIDE PRIDE:0000683 IHMC medication code Can include multiple medication codes. MIXS:0000884 PRIDE:PRIDE 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 PRIDE PRIDE:0000684 chemical administration 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 PRIDE:PRIDE Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867 PRIDE PRIDE:0000685 host body site Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867 PRIDE:PRIDE Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888 PRIDE PRIDE:0000686 host body product Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888 PRIDE:PRIDE Total mass of the host at collection, the unit depends on host. MIXS:0000263 PRIDE PRIDE:0000687 host total mass Total mass of the host at collection, the unit depends on host. MIXS:0000263 PRIDE:PRIDE The height of subject. MIXS:0000264 body height PRIDE PRIDE:0000688 host height The height of subject. MIXS:0000264 PRIDE:PRIDE 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 PRIDE PRIDE:0000689 host diet 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 PRIDE:PRIDE Content of last meal and time since feeding; can include multiple values. MIXS:0000870 PRIDE PRIDE:0000690 host last meal Content of last meal and time since feeding; can include multiple values. MIXS:0000870 PRIDE:PRIDE Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872 family relationship PRIDE PRIDE:0000691 host family relationship Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872 PRIDE:PRIDE Observed genotype MIXS:0000365 PRIDE PRIDE:0000692 host genotype Observed genotype MIXS:0000365 PRIDE:PRIDE Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274 PRIDE PRIDE:0000693 host phenotype Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274 PRIDE:PRIDE Core body temperature of the host when sample was collected. MIXS:0000874 PRIDE PRIDE:0000694 host body temperature Core body temperature of the host when sample was collected. MIXS:0000874 PRIDE:PRIDE Body mass index, calculated as weight/(height)squared. MIXS:0000317 PRIDE PRIDE:0000695 host body-mass index Body mass index, calculated as weight/(height)squared. MIXS:0000317 PRIDE:PRIDE 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 PRIDE PRIDE:0000696 ethnicity 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 PRIDE:PRIDE Most frequent job performed by subject. MIXS:0000896 PRIDE PRIDE:0000697 host occupation Most frequent job performed by subject. MIXS:0000896 PRIDE:PRIDE Whether full medical history was collected. MIXS:0000897 PRIDE PRIDE:0000698 medical history performed Whether full medical history was collected. MIXS:0000897 PRIDE:PRIDE Resting pulse, measured as beats per minutes. MIXS:0000333 PRIDE PRIDE:0000699 host pulse Resting pulse, measured as beats per minutes. MIXS:0000333 PRIDE:PRIDE 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 PRIDE PRIDE:0000700 perturbation 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000701 salinity 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 PRIDE:PRIDE Oxygenation status of the sample. MIXS:0000753 PRIDE PRIDE:0000702 oxygenation status of sample Oxygenation status of the sample. MIXS:0000753 PRIDE:PRIDE Temperature of the sample at the time of sampling. MIXS:0000113 PRIDE PRIDE:0000703 temperature Temperature of the sample at the time of sampling. MIXS:0000113 PRIDE:PRIDE 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 PRIDE PRIDE:0000704 organism count 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 PRIDE:PRIDE Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110 PRIDE PRIDE:0000705 sample storage temperature Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110 PRIDE:PRIDE 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 PRIDE PRIDE:0000706 sample volume or weight for DNA extraction 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 PRIDE:PRIDE Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116 PRIDE PRIDE:0000707 sample storage duration Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116 PRIDE:PRIDE 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 PRIDE PRIDE:0000708 observed host symbionts 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 PRIDE:PRIDE Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755 PRIDE PRIDE:0000709 sample storage location Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755 PRIDE:PRIDE Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752 PRIDE PRIDE:0000710 miscellaneous parameter Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752 PRIDE:PRIDE 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 PRIDE PRIDE:0000711 depth 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000712 elevation 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 PRIDE:PRIDE Present state of sample site MIXS:0001080 PRIDE PRIDE:0000713 current land use Present state of sample site MIXS:0001080 PRIDE:PRIDE Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312 PRIDE PRIDE:0000714 current vegetation Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312 PRIDE:PRIDE Reference or method used in vegetation classification MIXS:0000314 PRIDE PRIDE:0000715 current vegetation method Reference or method used in vegetation classification MIXS:0000314 PRIDE:PRIDE Previous land use and dates MIXS:0000315 PRIDE PRIDE:0000716 history of previous land use Previous land use and dates MIXS:0000315 PRIDE:PRIDE Reference or method used in determining previous land use and dates MIXS:0000316 PRIDE PRIDE:0000717 history of previous land use method Reference or method used in determining previous land use and dates MIXS:0000316 PRIDE:PRIDE Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318 PRIDE PRIDE:0000718 history of crop rotation Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318 PRIDE:PRIDE Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639 PRIDE PRIDE:0000719 history of agrochemical additions Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639 PRIDE:PRIDE Note method(s) used for tilling MIXS:0001081 PRIDE PRIDE:0000720 history of tillage Note method(s) used for tilling MIXS:0001081 PRIDE:PRIDE Historical and/or physical evidence of fire MIXS:0001086 PRIDE PRIDE:0000721 history of fire Historical and/or physical evidence of fire MIXS:0001086 PRIDE:PRIDE Historical and/or physical evidence of flooding MIXS:0000319 PRIDE PRIDE:0000722 history of flooding Historical and/or physical evidence of flooding MIXS:0000319 PRIDE:PRIDE Unusual physical events that may have affected microbial populations MIXS:0000320 PRIDE PRIDE:0000723 history of extreme event Unusual physical events that may have affected microbial populations MIXS:0000320 PRIDE:PRIDE 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 PRIDE PRIDE:0000724 soil horizon 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 PRIDE:PRIDE Reference or method used in determining the horizon MIXS:0000321 PRIDE PRIDE:0000725 horizon method Reference or method used in determining the horizon MIXS:0000321 PRIDE:PRIDE Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322 PRIDE PRIDE:0000726 sieving Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322 PRIDE:PRIDE Water content measurement MIXS:0000185 PRIDE PRIDE:0000727 water content Water content measurement MIXS:0000185 PRIDE:PRIDE Reference or method used in determining the water content of soil MIXS:0000323 PRIDE PRIDE:0000728 water content method Reference or method used in determining the water content of soil MIXS:0000323 PRIDE:PRIDE Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325 PRIDE PRIDE:0000729 pooling of DNA extracts Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325 PRIDE:PRIDE Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327 PRIDE PRIDE:0000730 storage conditions Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327 PRIDE:PRIDE Link to climate resource MIXS:0000328 PRIDE PRIDE:0000731 link to climate information Link to climate resource MIXS:0000328 PRIDE:PRIDE Mean annual temperature MIXS:0000642 PRIDE PRIDE:0000732 mean annual temperature Mean annual temperature MIXS:0000642 PRIDE:PRIDE Mean seasonal temperature MIXS:0000643 PRIDE PRIDE:0000733 mean seasonal temperature Mean seasonal temperature MIXS:0000643 PRIDE:PRIDE 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 PRIDE PRIDE:0000734 mean annual precipitation 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000735 mean seasonal precipitation 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 PRIDE:PRIDE Link to digitized soil maps or other soil classification information MIXS:0000329 PRIDE PRIDE:0000736 link to classification information Link to digitized soil maps or other soil classification information MIXS:0000329 PRIDE:PRIDE 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 PRIDE PRIDE:0000737 soil taxonomic of FAO classification 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 PRIDE:PRIDE Soil classification based on local soil classification system MIXS:0000330 PRIDE PRIDE:0000738 soil taxonomic of local classification Soil classification based on local soil classification system MIXS:0000330 PRIDE:PRIDE Reference or method used in determining the local soil classification MIXS:0000331 PRIDE PRIDE:0000739 soil taxonomic of local classification method Reference or method used in determining the local soil classification MIXS:0000331 PRIDE:PRIDE 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 PRIDE PRIDE:0000740 slope gradient 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000741 slope aspect 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 PRIDE:PRIDE Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084 PRIDE PRIDE:0000742 profile position Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084 PRIDE:PRIDE Drainage classification from a standard system such as the USDA system MIXS:0001085 PRIDE PRIDE:0000743 drainage classification Drainage classification from a standard system such as the USDA system MIXS:0001085 PRIDE:PRIDE 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 PRIDE PRIDE:0000744 soil texture 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 PRIDE:PRIDE Reference or method used in determining soil texture MIXS:0000336 PRIDE PRIDE:0000745 soil texture method Reference or method used in determining soil texture MIXS:0000336 PRIDE:PRIDE Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001 PRIDE PRIDE:0000746 pH Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001 PRIDE:PRIDE Reference or method used in determining pH MIXS:0001106 PRIDE PRIDE:0000747 pH method Reference or method used in determining pH MIXS:0001106 PRIDE:PRIDE Concentration of organic matter MIXS:0000204 PRIDE PRIDE:0000748 organic matter Concentration of organic matter MIXS:0000204 PRIDE:PRIDE Total organic carbon content MIXS:0000533 PRIDE PRIDE:0000749 total organic carbon Total organic carbon content MIXS:0000533 PRIDE:PRIDE Reference or method used in determining total organic carbon MIXS:0000337 PRIDE PRIDE:0000750 total organic carbon method Reference or method used in determining total organic carbon MIXS:0000337 PRIDE:PRIDE Total nitrogen content of the sample MIXS:0000530 PRIDE PRIDE:0000751 total nitrogen content Total nitrogen content of the sample MIXS:0000530 PRIDE:PRIDE Reference or method used in determining the total nitrogen MIXS:0000338 PRIDE PRIDE:0000752 total nitrogen content method Reference or method used in determining the total nitrogen MIXS:0000338 PRIDE:PRIDE 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 PRIDE PRIDE:0000753 microbial biomass 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 PRIDE:PRIDE Reference or method used in determining microbial biomass MIXS:0000339 PRIDE PRIDE:0000754 microbial biomass method Reference or method used in determining microbial biomass MIXS:0000339 PRIDE:PRIDE Link to additional analysis results performed on the sample MIXS:0000340 PRIDE PRIDE:0000755 links to additional analysis Link to additional analysis results performed on the sample MIXS:0000340 PRIDE:PRIDE Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652 PRIDE PRIDE:0000756 extreme unusual properties of heavy metals Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652 PRIDE:PRIDE Reference or method used in determining heavy metals MIXS:0000343 PRIDE PRIDE:0000757 extreme unusual properties of heavy metals method Reference or method used in determining heavy metals MIXS:0000343 PRIDE:PRIDE Aluminum saturation (esp. For tropical soils) MIXS:0000607 PRIDE PRIDE:0000758 extreme unusual properties of AI saturation Aluminum saturation (esp. For tropical soils) MIXS:0000607 PRIDE:PRIDE Reference or method used in determining Al saturation MIXS:0000324 PRIDE PRIDE:0000759 extreme unusual properties of AI saturation method Reference or method used in determining Al saturation MIXS:0000324 PRIDE:PRIDE Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421 PRIDE PRIDE:0000760 alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421 PRIDE:PRIDE Method used for alkalinity measurement MIXS:0000298 PRIDE PRIDE:0000761 alkalinity method Method used for alkalinity measurement MIXS:0000298 PRIDE:PRIDE Concentration of alkyl diethers MIXS:0000490 PRIDE PRIDE:0000762 alkyl diethers Concentration of alkyl diethers MIXS:0000490 PRIDE:PRIDE Measurement of aminopeptidase activity MIXS:0000172 PRIDE PRIDE:0000763 aminopeptidase activity Measurement of aminopeptidase activity MIXS:0000172 PRIDE:PRIDE Concentration of ammonium in the sample MIXS:0000427 PRIDE PRIDE:0000764 ammonium Concentration of ammonium in the sample MIXS:0000427 PRIDE:PRIDE Measurement of atmospheric data; can include multiple data MIXS:0001097 PRIDE PRIDE:0000765 atmospheric data Measurement of atmospheric data; can include multiple data MIXS:0001097 PRIDE:PRIDE Measurement of bacterial carbon production MIXS:0000173 PRIDE PRIDE:0000766 bacterial carbon production Measurement of bacterial carbon production MIXS:0000173 PRIDE:PRIDE Bacterial production in the water column measured by isotope uptake MIXS:0000683 PRIDE PRIDE:0000767 bacterial production Bacterial production in the water column measured by isotope uptake MIXS:0000683 PRIDE:PRIDE Measurement of bacterial respiration in the water column MIXS:0000684 PRIDE PRIDE:0000768 bacterial respiration Measurement of bacterial respiration in the water column MIXS:0000684 PRIDE:PRIDE Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174 PRIDE PRIDE:0000769 biomass Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174 PRIDE:PRIDE Concentration of bishomohopanol MIXS:0000175 PRIDE PRIDE:0000770 bishomohopanol Concentration of bishomohopanol MIXS:0000175 PRIDE:PRIDE Concentration of bromide MIXS:0000176 PRIDE PRIDE:0000771 bromide Concentration of bromide MIXS:0000176 PRIDE:PRIDE Concentration of calcium in the sample MIXS:0000432 PRIDE PRIDE:0000772 calcium Concentration of calcium in the sample MIXS:0000432 PRIDE:PRIDE Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310 PRIDE PRIDE:0000773 carbon nitrogen ratio Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310 PRIDE:PRIDE Concentration of chloride in the sample MIXS:0000429 PRIDE PRIDE:0000774 chloride Concentration of chloride in the sample MIXS:0000429 PRIDE:PRIDE Concentration of chlorophyll MIXS:0000177 PRIDE PRIDE:0000775 chlorophyll Concentration of chlorophyll MIXS:0000177 PRIDE:PRIDE Electrical conductivity of water MIXS:0000692 PRIDE PRIDE:0000776 conductivity Electrical conductivity of water MIXS:0000692 PRIDE:PRIDE Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435 PRIDE PRIDE:0000777 density Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435 PRIDE:PRIDE Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178 PRIDE PRIDE:0000778 diether lipids Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178 PRIDE:PRIDE Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436 PRIDE PRIDE:0000779 dissolved carbon dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436 PRIDE:PRIDE Concentration of dissolved hydrogen MIXS:0000179 PRIDE PRIDE:0000780 dissolved hydrogen Concentration of dissolved hydrogen MIXS:0000179 PRIDE:PRIDE Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434 PRIDE PRIDE:0000781 dissolved inorganic carbon Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434 PRIDE:PRIDE Concentration of dissolved inorganic nitrogen MIXS:0000698 PRIDE PRIDE:0000784 dissolved inorganic nitrogen Concentration of dissolved inorganic nitrogen MIXS:0000698 PRIDE:PRIDE Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106 PRIDE PRIDE:0000785 dissolved inorganic phosphorus Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106 PRIDE:PRIDE Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433 PRIDE PRIDE:0000786 dissolved organic carbon Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433 PRIDE:PRIDE Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162 PRIDE PRIDE:0000787 dissolved organic nitrogen Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162 PRIDE:PRIDE Concentration of dissolved oxygen MIXS:0000119 PRIDE PRIDE:0000788 dissolved oxygen Concentration of dissolved oxygen MIXS:0000119 PRIDE:PRIDE Visible waveband radiance and irradiance measurements in the water column MIXS:0000703 PRIDE PRIDE:0000789 downward PAR Visible waveband radiance and irradiance measurements in the water column MIXS:0000703 PRIDE:PRIDE Raw or converted fluorescence of water MIXS:0000704 PRIDE PRIDE:0000790 fluorescence Raw or converted fluorescence of water MIXS:0000704 PRIDE:PRIDE Measurement of glucosidase activity MIXS:0000137 PRIDE PRIDE:0000791 glucosidase activity Measurement of glucosidase activity MIXS:0000137 PRIDE:PRIDE Measurement of light intensity MIXS:0000706 PRIDE PRIDE:0000792 light intensity Measurement of light intensity MIXS:0000706 PRIDE:PRIDE Concentration of magnesium in the sample MIXS:0000431 PRIDE PRIDE:0000793 magnesium Concentration of magnesium in the sample MIXS:0000431 PRIDE:PRIDE Measurement of mean friction velocity MIXS:0000498 PRIDE PRIDE:0000794 mean friction velocity Measurement of mean friction velocity MIXS:0000498 PRIDE:PRIDE Measurement of mean peak friction velocity MIXS:0000502 PRIDE PRIDE:0000795 mean peak friction velocity Measurement of mean peak friction velocity MIXS:0000502 PRIDE:PRIDE Concentration of nitrate in the sample MIXS:0000425 PRIDE PRIDE:0000796 nitrate Concentration of nitrate in the sample MIXS:0000425 PRIDE:PRIDE Concentration of nitrite in the sample MIXS:0000426 PRIDE PRIDE:0000797 nitrite Concentration of nitrite in the sample MIXS:0000426 PRIDE:PRIDE Concentration of nitrogen (total) MIXS:0000504 PRIDE PRIDE:0000798 nitrogen Concentration of nitrogen (total) MIXS:0000504 PRIDE:PRIDE Concentration of organic carbon MIXS:0000508 PRIDE PRIDE:0000799 organic carbon Concentration of organic carbon MIXS:0000508 PRIDE:PRIDE Concentration of organic nitrogen MIXS:0000205 PRIDE PRIDE:0000800 organic nitrogen Concentration of organic nitrogen MIXS:0000205 PRIDE:PRIDE Concentration of particulate organic carbon MIXS:0000515 PRIDE PRIDE:0000801 particulate organic carbon Concentration of particulate organic carbon MIXS:0000515 PRIDE:PRIDE Concentration of particulate organic nitrogen MIXS:0000719 PRIDE PRIDE:0000802 particulate organic nitrogen Concentration of particulate organic nitrogen MIXS:0000719 PRIDE:PRIDE Concentration of petroleum hydrocarbon MIXS:0000516 PRIDE PRIDE:0000803 petroleum hydrocarbon Concentration of petroleum hydrocarbon MIXS:0000516 PRIDE:PRIDE Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180 PRIDE PRIDE:0000804 phaeopigments Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180 PRIDE:PRIDE Concentration of phosphate MIXS:0000505 PRIDE PRIDE:0000805 phosphate Concentration of phosphate MIXS:0000505 PRIDE:PRIDE Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181 PRIDE PRIDE:0000806 phospholipid fatty acid Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181 PRIDE:PRIDE Measurement of photon flux MIXS:0000725 PRIDE PRIDE:0000807 photon flux Measurement of photon flux MIXS:0000725 PRIDE:PRIDE Concentration of potassium in the sample MIXS:0000430 PRIDE PRIDE:0000808 potassium Concentration of potassium in the sample MIXS:0000430 PRIDE:PRIDE Pressure to which the sample is subject to, in atmospheres MIXS:0000412 PRIDE PRIDE:0000809 pressure Pressure to which the sample is subject to, in atmospheres MIXS:0000412 PRIDE:PRIDE Measurement of primary production, generally measured as isotope uptake MIXS:0000728 PRIDE PRIDE:0000810 primary production Measurement of primary production, generally measured as isotope uptake MIXS:0000728 PRIDE:PRIDE Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182 PRIDE PRIDE:0000811 redox potential Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182 PRIDE:PRIDE Concentration of silicate MIXS:0000184 PRIDE PRIDE:0000812 silicate Concentration of silicate MIXS:0000184 PRIDE:PRIDE 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 PRIDE PRIDE:0000813 size-fraction lower threshold 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 PRIDE:PRIDE 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 PRIDE PRIDE:0000814 size-fraction upper threshold 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 PRIDE:PRIDE Sodium concentration in the sample MIXS:0000428 PRIDE PRIDE:0000815 sodium Sodium concentration in the sample MIXS:0000428 PRIDE:PRIDE Concentration of soluble reactive phosphorus MIXS:0000738 PRIDE PRIDE:0000816 soluble reactive phosphorus Concentration of soluble reactive phosphorus MIXS:0000738 PRIDE:PRIDE Concentration of sulfate in the sample MIXS:0000423 PRIDE PRIDE:0000817 sulfate Concentration of sulfate in the sample MIXS:0000423 PRIDE:PRIDE Concentration of sulfide in the sample MIXS:0000424 PRIDE PRIDE:0000818 sulfide Concentration of sulfide in the sample MIXS:0000424 PRIDE:PRIDE Concentration of suspended particulate matter MIXS:0000741 PRIDE PRIDE:0000819 suspended particulate matter Concentration of suspended particulate matter MIXS:0000741 PRIDE:PRIDE Stage of tide MIXS:0000750 PRIDE PRIDE:0000820 tidal stage Stage of tide MIXS:0000750 PRIDE:PRIDE Measurement of total depth of water column MIXS:0000634 PRIDE PRIDE:0000821 total depth of water column Measurement of total depth of water column MIXS:0000634 PRIDE:PRIDE Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744 PRIDE PRIDE:0000822 total dissolved nitrogen Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744 PRIDE:PRIDE Total inorganic nitrogen content MIXS:0000745 PRIDE PRIDE:0000823 total inorganic nitrogen Total inorganic nitrogen content MIXS:0000745 PRIDE:PRIDE 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 PRIDE PRIDE:0000824 total nitrogen concentration 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 PRIDE:PRIDE Total particulate carbon content MIXS:0000747 PRIDE PRIDE:0000825 total particulate carbon Total particulate carbon content MIXS:0000747 PRIDE:PRIDE Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117 PRIDE PRIDE:0000826 total phosphorus Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117 PRIDE:PRIDE Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191 PRIDE PRIDE:0000827 turbidity Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191 PRIDE:PRIDE 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 PRIDE PRIDE:0000828 soil 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 PRIDE:PRIDE A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment PRIDE PRIDE:0000829 water A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment PRIDE:PRIDE 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 PRIDE PRIDE:0000830 Olink Reveal 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 PRIDE:PRIDE 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. NCIT:C171252 PRIDE PRIDE:0000831 file_format 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. PRIDE:PRIDE A checklist of columns and properties that will be applied during a validation process to an SDRF or other PSI standard PRIDE PRIDE:0000832 template A checklist of columns and properties that will be applied during a validation process to an SDRF or other PSI standard PRIDE:PRIDE The specific version of a template PRIDE PRIDE:0000833 template_version The specific version of a template PRIDE:PRIDE A hash generated after validating an SDRF dataset; this is helpful to understand if one file has been validated or not PRIDE PRIDE:0000834 validation_hash A hash generated after validating an SDRF dataset; this is helpful to understand if one file has been validated or not PRIDE:PRIDE An accession to a cellosaurus cell line that could be use to annotate SDRF samples PRIDE PRIDE:0000835 cellosaurus accession An accession to a cellosaurus cell line that could be use to annotate SDRF samples PRIDE:PRIDE A name to a cellosaurus cell line that could be use to annotate SDRF samples PRIDE PRIDE:0000836 cellosaurus name A name to a cellosaurus cell line that could be use to annotate SDRF samples PRIDE:PRIDE