From a72a029e63130dcd90fa1ef988354308e9669cfa Mon Sep 17 00:00:00 2001 From: GitHub Date: Thu, 12 Oct 2023 15:39:03 +0000 Subject: [PATCH] Update PRIDE OWL file --- pride_cv.owl | 10910 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 10910 insertions(+) create mode 100644 pride_cv.owl diff --git a/pride_cv.owl b/pride_cv.owl new file mode 100644 index 0000000..1a0ef8b --- /dev/null +++ b/pride_cv.owl @@ -0,0 +1,10910 @@ + + + + + OBO-Edit 2.3.1 + 23:09:2022 11:38 + PRIDE + 1.2 + Yasset Perez-Riverol + I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd:string, ...) + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PRIDE + http://purl.obolibrary.org/obo/PRIDE_part_of + part_of + + + + + + + + PRIDE + has_units + has_units + + + + + + + + + PRIDE + part_of + part_of + + + + + + + + + + + + + + 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 + yperez + 2020-03-16T18:01:06Z + PRIDE + MS:1000451 + mass analyzer + + + + + mass analyzer + PRIDE:PRIDE + + + + + + + + + A sample that has not been labelled or modified + yperez + 2020-05-12T11:58:52Z + PRIDE + MS:1002038 + label free sample + + + + + A sample that has not been labelled or modified + PRIDE:PRIDE + + + + + + + + + The date on which data creation began [NCI] + ypriverol + 2018-08-29T14:52:49Z + PRIDE + NCIT:C69199 + Content Creation date + + + + + The date on which data creation began [NCI] + PRIDE:PRIDE + + + + + + + + PRIDE + PRIDE:0000000 + Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam + Reference additional parameter + + + + + + + + PRIDE + PRIDE:0000001 + Root node for terms relating to the description of a protocol as ordered steps, in relation to the PRIDE.xml element ExperimentCollection/Experiment/Protocol/ProtocolSteps/StepDescription + Protocol step description additional parameter + + + + + + + + PRIDE + PRIDE:0000002 + Root node for terms relating to the description of a ModificationItem (post translational modification or artifactual modification) in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/ModificationItem/additional/cvParam + ModificationItem additional parameter + + + + + + + + PRIDE + PRIDE:0000003 + Root node for terms relating to the description of a PeptideItem in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/additional/cvParam + Peptide item additional parameter + + + + + + + + PRIDE + PRIDE:0000004 + Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam + Identification additional parameter + + + + + + + + PRIDE + PRIDE:0000005 + Root node for terms relating to the description of a Gel in relation to the PRIDE.xml element ExperimentCollection/Experiment/TwoDimensionalIdentification/Gel/additional/cvParam + Gel additional parameter + + + + + + + + PRIDE + PRIDE:0000006 + Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam + Experiment additional parameter + + + + + + + + PRIDE + PRIDE:0000007 + Version number / identifier for search engine. + SearchEngineVersion + true + + + + + + + + + PRIDE + PRIDE:0000008 + Protein search engine output parameter + + + + + + + + + + PRIDE + PRIDE:0000009 + Ion mass tolerance + + + + + + + + + PRIDE + PRIDE:0000010 + PrecursorIon mass tolerance + + + + + + + + + PRIDE + PRIDE:0000011 + MS2 ion mass tolerance + + + + + + + + + + + + + + + + 1.0 - normalized correlation score. + PRIDE + PRIDE:0000012 + Delta Cn + + + + + 1.0 - normalized correlation score. + PRIDE:PRIDE + + + + + + + + + + PRIDE + PRIDE:0000013 + X correlation + + + + + + + + + PRIDE + PRIDE:0000014 + X correlation (+1) + + + + + + + + + PRIDE + PRIDE:0000015 + X correlation (+2) + + + + + + + + + PRIDE + PRIDE:0000016 + X correlation (+3) + + + + + + + + PRIDE + PRIDE:0000017 + Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam + Sample description additional parameter + + + + + + + + + PRIDE + PRIDE:0000018 + 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. + Disease free + + + + + + + + + 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 + + + + + + + + + PRIDE + PRIDE:0000025 + Reduction + + + + + + + + + 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 + + + + + + + + PRIDE + PRIDE:0000028 + Valid values for cvLabel entries referencing external database / CV / ontology. + Cv Label + + + + + + + + + PRIDE + PRIDE:0000029 + Valid value for the cvLabel entry referencing PubMed. + PubMed + + + + + + + + + PRIDE + PRIDE:0000030 + Valid value for the cvLabel entry referencing PRIDE + PRIDE + + + + + + + + + PRIDE + PRIDE:0000031 + Valid value for the cvLabel entry referencing GO. + GO + + + + + + + + + PRIDE + PRIDE:0000032 + Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH) + MeSH + + + + + + + + + PRIDE + PRIDE:0000033 + Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy. + NEWT + + + + + + + + + PRIDE + PRIDE:0000034 + Valid value for the cvLabel entry referencing the PSI ontology + PSI + + + + + + + + + PRIDE + PRIDE:0000035 + Valid value for the cvLabel entry referencing UNIMOD + UNIMOD + + + + + + + + + PRIDE + PRIDE:0000036 + Valid value for the cvLabel entry referencing RESID. + RESID + + + + + + + + + PRIDE + PRIDE:0000037 + Staining + + + + + + + + + PRIDE + PRIDE:0000038 + Valid value for the cvLabel entry referencing ISBN + ISBN + + + + + + + + + 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 + + + + + + + + + PRIDE + PRIDE:0000040 + This CV term should be used in association with a value that is a free-text description of the experiment. + Experiment description + + + + + + + + + PRIDE + PRIDE:0000041 + Search database protein sequence + + + + + + + + + PRIDE + PRIDE:0000042 + DOI + + + + + + + + + PRIDE + PRIDE:0000043 + FIX + + + + + + + + PRIDE + PRIDE:0000044 + Search algorithm + + + + + + + + + + PRIDE + PRIDE:0000045 + Sequest + + + + + + + + + + + PRIDE + PRIDE:0000046 + Mascot + + + + + + + + + + PRIDE + PRIDE:0000047 + Really X + XTandem + + + + + + + + PRIDE + PRIDE:0000048 + OutputParameter + true + + + + + + + + + PRIDE + PRIDE:0000049 + Peptide search engine output parameter + + + + + + + + + + + + + + + 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 + C*10^4 + 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 + + + + + + + + + + PRIDE + PRIDE:0000056 + Bioworks + + + + + + + + + + + + + + + Molecular weight of a protein. + PRIDE + PRIDE:0000057 + Molecular weight + + + + + Molecular weight of a protein. + PRIDE:PRIDE + + + + + + + + + + + + + + + PRIDE + PRIDE:0000058 + z + + + + + + + + + PRIDE + PRIDE:0000059 + File + + + + + + + + + PRIDE + PRIDE:0000060 + Scan + + + + + + + + + + + + + + + PRIDE + PRIDE:0000061 + Coverage + + + + + + + + + + + + + + + PRIDE + PRIDE:0000062 + rsp + + + + + + + + + PRIDE + PRIDE:0000063 + Protein description line + + + + + + + + + PRIDE + PRIDE:0000064 + Secondary accession + + + + + + + + + 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 + + + + + + + + + PRIDE + PRIDE:0000067 + Reference reporting this experiment + + + + + + + + + PRIDE + PRIDE:0000068 + Reference describing sample preparation + + + + + + + + + + + + + + + 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 + + + + + + + + + + PRIDE + PRIDE:0000071 + Search engine setting + + + + + + + + + PRIDE + PRIDE:0000072 + Fixed modification setting + + + + + + + + + PRIDE + PRIDE:0000073 + Variable modification setting + + + + + + + + + PRIDE + PRIDE:0000074 + Maximum Missed Cleavages Setting + + + + + + + + + PRIDE + PRIDE:0000075 + Mass value type setting + + + + + + + + + PRIDE + PRIDE:0000076 + Mass value type setting monoisotopic + + + + + + + + + PRIDE + PRIDE:0000077 + Mass value type setting average + + + + + + + + + PRIDE + PRIDE:0000078 + Peptide mass tolerance setting + + + + + + + + + PRIDE + PRIDE:0000079 + Accurate mass mode setting + + + + + + + + + PRIDE + PRIDE:0000080 + Accurate mass mode setting true + + + + + + + + + PRIDE + PRIDE:0000081 + Accurate mass mode setting false + + + + + + + + + PRIDE + PRIDE:0000082 + Mass error type setting + + + + + + + + + PRIDE + PRIDE:0000083 + mass error type setting ppm + + + + + + + + + PRIDE + PRIDE:0000084 + mass error type setting mmu + + + + + + + + + PRIDE + PRIDE:0000085 + mass error type setting percent + + + + + + + + + PRIDE + PRIDE:0000086 + mass error type setting Daltons + + + + + + + + + PRIDE + PRIDE:0000087 + Protonated setting + + + + + + + + + PRIDE + PRIDE:0000088 + Protonated setting MH+ + + + + + + + + + PRIDE + PRIDE:0000089 + Protonated setting Mr + + + + + + + + + PRIDE + PRIDE:0000090 + Protonated setting M-H- + + + + + + + + + PRIDE + PRIDE:0000091 + Rank + + + + + + + + + PRIDE + PRIDE:0000092 + All peptides matched + + + + + + + + + PRIDE + PRIDE:0000093 + All peptides matched true + + + + + + + + + PRIDE + PRIDE:0000094 + All peptides matched false + + + + + + + + + PRIDE + PRIDE:0000095 + Masses matched + + + + + + + + + PRIDE + PRIDE:0000096 + Reported Chromosome + + + + + + + + + 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 + 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 + + + + + + + + + + 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 + + + + + + + + + PRIDE + PRIDE:0000114 + The name of the sample labelled with iTRAQ reagent 114. + iTRAQ reagent 114 + + + + + + + + + PRIDE + PRIDE:0000115 + The name of the sample labelled with iTRAQ reagent 115. + iTRAQ reagent 115 + + + + + + + + + PRIDE + PRIDE:0000116 + The name of the sample labelled with iTRAQ reagent 116. + iTRAQ reagent 116 + + + + + + + + + PRIDE + PRIDE:0000117 + The name of the sample labelled with iTRAQ reagent 117. + iTRAQ reagent 117 + + + + + + + + + + PRIDE + PRIDE:0000118 + The intensity of the sample labelled with iTRAQ reagent 114. + iTRAQ intensity 114 + + + + + + + + + + PRIDE + PRIDE:0000119 + The intensity of the sample labelled with iTRAQ reagent 115. + iTRAQ intensity 115 + + + + + + + + + + PRIDE + PRIDE:0000120 + The intensity of the sample labelled with iTRAQ reagent 116. + iTRAQ intensity 116 + + + + + + + + + + PRIDE + PRIDE:0000121 + The intensity of the sample labelled with iTRAQ reagent 117. + iTRAQ intensity 117 + + + + + + + + + A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures. + 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 + This value associated with this CV term should always be in centimeters. + 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 + This CV term should be used in association with a value that is a free-text description of the first dimension details + 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 + This CV term should be used in association with a value that is a free-text description of the second dimension details + Second dimension details + + + + + Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis. + PRIDE:PRIDE + + + + + + + + Obsoleted terms. + PRIDE + PRIDE:0000130 + Obsoleted parameters + true + + + + + Obsoleted terms. + Curator:Rc + + + + + + + + + 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 + + + + + + + + + + + + + + + PRIDE + PRIDE:0000146 + PepSplice precision + + + + + + + + + + + + + + + PRIDE + PRIDE:0000147 + PepSplice False Discovery Rate + + + + + + + + + + + + + + + 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 ID + PRIDE + PRIDE:0000156 + Project identifier + + + + + unique identifier of project. + PRIDE:PRIDE + + + + + + + + + type of search. + PRIDE + PRIDE:0000157 + Search type + + + + + type of search. + PRIDE:PRIDE + + + + + + + + + PRIDE + PRIDE:0000158 + MS search + + + + + + + + + PRIDE + PRIDE:0000159 + MS/MS search + + + + + + + + + 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 + + + + + + + + + + PRIDE + PRIDE:0000168 + Nucleic acid sequence + + + + + + + + + + PRIDE + PRIDE:0000169 + Start position of the nucleic acid sequence on the chromosome + + + + + + + + + + PRIDE + PRIDE:0000170 + Stop position of the nucleic acid sequence on the chromosome + + + + + + + + + PRIDE + PRIDE:0000171 + funding reference + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + Mass. + fragment ion mass + PRIDE + PRIDE:0000188 + product ion m/z + + + + + Mass. + PRIDE:PRIDE + + + + + + + + + Intensity. + fragment ion intensity + PRIDE + PRIDE:0000189 + product ion intensity + + + + + Intensity. + PRIDE:PRIDE + + + + + + + + + Mass error. + fragment ion mass error + PRIDE + PRIDE:0000190 + product ion mass error + + + + + Mass error. + PRIDE:PRIDE + + + + + + + + + Retention time error in minutes. + fragment ion retention time error + PRIDE + PRIDE:0000191 + product ion retention time error + + + + + Retention time error in minutes. + PRIDE:PRIDE + + + + + + + + + Product ion type. + fragment ion type + PRIDE + PRIDE:0000192 + product ion type + + + + + Product ion type. + PRIDE:PRIDE + + + + + + + + + Y ion type. + y fragment ion + PRIDE + PRIDE:0000193 + y ion + + + + + Y ion type. + PRIDE:PRIDE + + + + + + + + + B ion type. + b fragment ion + PRIDE + PRIDE:0000194 + b ion + + + + + B ion type. + PRIDE: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 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 + + + + + + + + + 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 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + A general term for any stable isotope method. + PRIDE + PRIDE:0000205 + Heavy stable isotope label + true + + + + + A general term for any stable isotope method. + PRIDE:PRIDE + + + + + + + + The precise amino acid that has been modified. + PRIDE + PRIDE:0000206 + Heavy stable isotope label residue + true + + + + + The precise amino acid that has been modified. + PRIDE:PRIDE + + + + + + + + A general term for any stable isotope method. + PRIDE + PRIDE:0000207 + Light stable isotope label + true + + + + + A general term for any stable isotope method. + PRIDE:PRIDE + + + + + + + + The precise amino acid that has been modified. + PRIDE + PRIDE:0000208 + Light stable isotope label residue + true + + + + + 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 + + + + + + + + + Retention time error in minutes. + PRIDE + PRIDE:0000221 + parent ion retention time error + + + + + Retention time error in minutes. + PRIDE:PRIDE + + + + + + + + + average iTRAQ ratio sample over control. + PRIDE + PRIDE:0000222 + spectrum iTRAQ ratio + true + + + + + average iTRAQ ratio sample over control. + PRIDE:PRIDE + + + + + + + + + Average spectrum iTRAQ ratio (=geometric mean) for the peptide. + PRIDE + PRIDE:0000223 + peptide iTRAQ ratio average + true + + + + + Average spectrum iTRAQ ratio (=geometric mean) for the peptide. + PRIDE:PRIDE + + + + + + + + + Average spectrum iTRAQ ratio (=geometric mean) for the protein. + PRIDE + PRIDE:0000224 + protein iTRAQ ratio average + true + + + + + Average spectrum iTRAQ ratio (=geometric mean) for the protein. + PRIDE:PRIDE + + + + + + + + + Number of quantified spectra contributing to the protein iTRAQ ratio. + PRIDE + PRIDE:0000225 + protein iTRAQ ratio number of contributing spectra + true + + + + + Number of quantified spectra contributing to the protein iTRAQ ratio. + PRIDE:PRIDE + + + + + + + + + Geometric sample standard deviation of the protein iTRAQ ratio. + PRIDE + PRIDE:0000226 + protein iTRAQ ratio standard deviation + true + + + + + Geometric sample standard deviation of the protein iTRAQ ratio. + PRIDE:PRIDE + + + + + + + + + X ion type. + x fragment ion + PRIDE + PRIDE:0000227 + x ion + + + + + X ion type. + PRIDE: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 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 + + + + + + + + + Z ion type. + z fragment ion + PRIDE + PRIDE:0000230 + z ion + + + + + Z ion type. + PRIDE: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 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 + + + + + + + + + A ion type. + a fragment ion + PRIDE + PRIDE:0000233 + a ion + + + + + A ion type. + PRIDE: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 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 + + + + + + + + + C ion type. + c fragment ion + PRIDE + PRIDE:0000236 + c ion + + + + + C ion type. + PRIDE: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 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + Precursor ion. + parent ion + PRIDE + PRIDE:0000263 + precursor ion + + + + + Precursor ion. + PRIDE:PRIDE + + + + + + + + + PRIDE + PRIDE:0000264 + The name of the sample labelled with iTRAQ reagent 113 + iTRAQ reagent 113 + + + + + + + + + PRIDE + PRIDE:0000265 + The name of the sample labelled with iTRAQ reagent 118 + iTRAQ reagent 118 + + + + + + + + + PRIDE + PRIDE:0000266 + The name of the sample labelled with iTRAQ reagent 119 + iTRAQ reagent 119 + + + + + + + + + PRIDE + PRIDE:0000267 + The name of the sample labelled with iTRAQ reagent 121 + iTRAQ reagent 121 + + + + + + + + + + PRIDE + PRIDE:0000268 + The intensity of the sample labelled with iTRAQ reagent 113 + iTRAQ intensity 113 + + + + + + + + + + PRIDE + PRIDE:0000269 + The intensity of the sample labelled with iTRAQ reagent 118 + iTRAQ intensity 118 + + + + + + + + + + PRIDE + PRIDE:0000270 + The intensity of the sample labelled with iTRAQ reagent 119 + iTRAQ intensity 119 + + + + + + + + + + PRIDE + PRIDE:0000271 + The intensity of the sample labelled with iTRAQ reagent 121 + iTRAQ intensity 121 + + + + + + + + + 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 + + + + + + + + + PRIDE + PRIDE:0000273 + SloMo score threshold for valid modification location + + + + + + + + + PRIDE + PRIDE:0000274 + MaxQuant percentage threshold for valid modification location + + + + + + + + + PRIDE + PRIDE:0000275 + SloMo score + + + + + + + + + PRIDE + PRIDE:0000276 + MaxQuant percentage + + + + + + + + + PRIDE + PRIDE:0000277 + Valid location + + + + + + + + PRIDE + PRIDE:0000278 + Processing method additional parameter + + + + + + + + + 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 + + + + + + + + + Z ion type with two extra protons + zHH fragment ion + PRIDE + PRIDE:0000281 + zHH ion + + + + + Z ion type with two extra protons + PRIDE: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 + + + + + + + + + PRIDE + PRIDE:0000285 + The name of the sample labelled with TMT reagent 126 + TMT reagent 126 + + + + + + + + + PRIDE + PRIDE:0000286 + The name of the sample labelled with TMT reagent 127 + TMT reagent 127 + + + + + + + + + PRIDE + PRIDE:0000287 + The name of the sample labelled with TMT reagent 128 + TMT reagent 128 + + + + + + + + + PRIDE + PRIDE:0000288 + The name of the sample labelled with TMT reagent 129 + TMT reagent 129 + + + + + + + + + PRIDE + PRIDE:0000289 + The name of the sample labelled with TMT reagent 130 + TMT reagent 130 + + + + + + + + + PRIDE + PRIDE:0000290 + The name of the sample labelled with TMT reagent 131 + TMT reagent 131 + + + + + + + + + + PRIDE + PRIDE:0000291 + The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS] + TMT intensity 126 + + + + + + + + + + PRIDE + PRIDE:0000292 + The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS] + TMT intensity 127 + + + + + + + + + + PRIDE + PRIDE:0000293 + The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS] + TMT intensity 128 + + + + + + + + + + PRIDE + PRIDE:0000294 + The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS] + TMT intensity 129 + + + + + + + + + + PRIDE + PRIDE:0000295 + The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS] + TMT intensity 130 + + + + + + + + + + PRIDE + PRIDE:0000296 + The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS] + TMT intensity 131 + + + + + + + + + PRIDE + PRIDE:0000297 + Name of the gene that has been identified (if a nucleotide database was used to perform the search) + Gene name + + + + + + + + + PRIDE + PRIDE:0000298 + Position of the modification in the protein sequence + Modification Position in Protein Sequence + + + + + + + + + PRIDE + PRIDE:0000299 + The original submitted protein accession for this identification. This might have been curated as part of the submission process. + Submitted Protein Accession + + + + + + + + + The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication. + jg + 2011-05-12T11:32:07Z + 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). + jg + 2011-05-12T11:39:59Z + 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). + jg + 2011-05-12T11:50:00Z + 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. + jg + 2011-05-12T11:58:52Z + PRIDE + PRIDE:0000303 + Decoy hit + true + + + + + 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. + jg + 2011-05-25T11:22:05Z + 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. + jg + 2011-05-25T05:44:24Z + PRIDE + PRIDE:0000305 + Gel-based experiment + + + + + Defines a gel-based proteomics experiment. + PRIDE:PRIDE + + + + + + + + + PRIDE + PRIDE:0000306 + Experiment.[Curator:ACSORDAS] + Imported from NCBI Peptidome + + + + + + + + + jg + 2011-07-22T09:15:33Z + PRIDE + PRIDE:0000307 + Defines various quantification methods + Quantification method + + + + + + + + + jg + 2011-07-22T09:16:24Z + PRIDE + PRIDE:0000308 + Describes gel-based quantification methods + Gel-based quantification method + + + + + + + + + jg + 2011-07-22T09:17:03Z + PRIDE + PRIDE:0000309 + Describes gel-free quantification methods + Gel-free quantification method + + + + + + + + + jg + 2011-07-22T09:17:34Z + PRIDE + PRIDE:0000310 + Describes quantification techniques using isotope labeling + Isotope labeling + + + + + + + + + jg + 2011-07-22T09:18:39Z + PRIDE + PRIDE:0000311 + Describes quantification techniques based on selected / multiple reaction monitoring + Selected Reaction Monitoring + + + + + + + + + jg + 2011-07-22T09:19:54Z + PRIDE + PRIDE:0000312 + Describes label free quantification techniques. + Label free + + + + + + + + + jg + 2011-07-22T09:20:23Z + PRIDE + PRIDE:0000313 + Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level + iTRAQ + + + + + + + + + jg + 2011-07-22T09:23:12Z + Tandem Mass Tag + PRIDE + PRIDE:0000314 + Tandem Mass Tag is a MS2 based isotope labeling quantification technique + TMT + + + + + + + + + jg + 2011-07-22T09:25:50Z + Stable isotope labeling with amino acids in cell culture + PRIDE + PRIDE:0000315 + Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification + SILAC + + + + + + + + + jg + 2011-07-22T09:28:05Z + PRIDE + PRIDE:0000316 + Describes isotope labeling quantification techniques detectable at MS1 level. + MS1 based isotope labeling + + + + + + + + + jg + 2011-07-22T09:29:15Z + PRIDE + PRIDE:0000317 + Describes isotope labeling quantification techniques detectable at MS1 level. + MS2 based isotope labeling + + + + + + + + + jg + 2011-07-22T09:30:12Z + PRIDE + PRIDE:0000318 + The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. + 18O + + + + + + + + + jg + 2011-07-22T09:31:24Z + Isotope-Coded Affinity Tags + PRIDE + PRIDE:0000319 + Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. + ICAT + + + + + + + + + jg + 2011-07-22T09:32:46Z + PRIDE + PRIDE:0000320 + AQUA is an isotope labeling based quantification technique that uses known peptides. + AQUA + + + + + + + + + jg + 2011-07-22T09:34:37Z + Isotope-coded protein label + PRIDE + PRIDE:0000321 + Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. + ICPL + + + + + + + + + jg + 2011-07-22T09:36:57Z + Exponentially Modified Protein Abundance Index + PRIDE + PRIDE:0000322 + 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. + emPAI + + + + + + + + + jg + 2011-07-22T09:38:17Z + Total Ion Current + PRIDE + PRIDE:0000323 + The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. + TIC + + + + + + + + + + jg + 2011-07-22T09:43:30Z + PRIDE + PRIDE:0000324 + A reagent used for quantification. + Quantification reagent + + + + + + + + + + jg + 2011-07-22T09:44:18Z + PRIDE + PRIDE:0000325 + The heavy label used in SILAC experiments. + SILAC heavy + + + + + + + + + + jg + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000326 + The light reagent used in SILAC experiments. + SILAC light + + + + + + + + + + jg + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000327 + The medium weight reagent used in SILAC experiments. + SILAC medium + + + + + + + + + jg + 2011-07-22T09:48:42Z + PRIDE + PRIDE:0000328 + Reagent used in SILAC labeling. + SILAC reagent + + + + + + + + + jg + 2011-07-22T09:49:46Z + PRIDE + PRIDE:0000329 + Reagent used in iTRAQ experiments. + iTRAQ reagent + + + + + + + + + jg + 2012-03-06T11:32:24Z + PRIDE + PRIDE:0000330 + 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. + Arbitrary quantification unit + + + + + + + + + jg + 2012-03-06T11:33:13Z + PRIDE + PRIDE:0000331 + Quantification values reported as arbitrary counts (most often ion counts). + Counts + + + + + + + + + jg + 2011-07-22T10:08:04Z + PRIDE + PRIDE:0000337 + Reagent used in TMT experiments. + TMT reagent + + + + + + + + + jg + 2011-07-22T10:19:04Z + PRIDE + PRIDE:0000344 + Reagent used in ICAT experiments. + ICAT reagent + + + + + + + + + jg + 2011-07-22T10:19:38Z + PRIDE + PRIDE:0000345 + ICAT light reagent + + + + + + + + + jg + 2011-07-22T10:19:38Z + PRIDE + PRIDE:0000346 + ICAT heavy reagent + + + + + + + + + jg + 2011-07-22T10:22:42Z + PRIDE + PRIDE:0000347 + Reagent used in ICPL experiments. + ICPL reagent + + + + + + + + + jg + 2011-07-22T10:24:42Z + PRIDE + PRIDE:0000348 + ICPL 0 reagent + + + + + + + + + jg + 2011-07-22T10:24:42Z + PRIDE + PRIDE:0000349 + ICPL 4 reagent + + + + + + + + + jg + 2011-07-22T10:24:42Z + PRIDE + PRIDE:0000350 + ICPL 6 reagent + + + + + + + + + jg + 2011-07-22T10:24:42Z + PRIDE + PRIDE:0000351 + ICPL 10 reagent + + + + + + + + + jg + 2011-07-22T10:26:08Z + PRIDE + PRIDE:0000352 + Parameters to report quantification values. + Quantification value + + + + + + + + + + + jg + 2011-07-22T10:26:33Z + PRIDE + PRIDE:0000353 + Parameters describing quantification values for multiplexed samples. + Multiplexed quantification value + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000354 + Intensity subsample 1 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000355 + Intensity subsample 2 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000356 + Intensity subsample 3 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000357 + Intensity subsample 4 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000358 + Intensity subsample 5 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000359 + Intensity subsample 6 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000360 + Intensity subsample 7 + + + + + + + + + jg + 2011-07-22T10:27:30Z + PRIDE + PRIDE:0000361 + Intensity subsample 8 + + + + + + + + + jg + 2011-07-22T10:55:31Z + PRIDE + PRIDE:0000362 + Values from other quantification techniques. + Other quantification value + + + + + + + + + + jg + 2011-07-22T10:55:56Z + PRIDE + PRIDE:0000363 + The emPAI for the protein. + emPAI value + + + + + + + + + + + jg + 2011-07-22T10:57:36Z + PRIDE + PRIDE:0000364 + The Total Ion Count for the given entity. + TIC value + + + + + + + + + jg + 2011-07-22T10:59:57Z + PRIDE + PRIDE:0000365 + Describes multiples subsamples. + Multiplexed sample description + + + + + + + + + jg + 2011-07-22T11:00:32Z + PRIDE + PRIDE:0000366 + Identifies samples that are made up of multiplexed subsamples. + Contains multiple subsamples + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000367 + Subsample 1 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000368 + Subsample 2 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000369 + Subsample 3 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000370 + Subsample 4 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000371 + Subsample 5 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000372 + Subsample 6 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000373 + Subsample 7 description + + + + + + + + + jg + 2011-07-22T11:02:56Z + PRIDE + PRIDE:0000374 + Subsample 8 description + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000375 + Standard deviation subsample 1 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000376 + Standard deviation subsample 2 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000377 + Standard deviation subsample 3 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000378 + Standard deviation subsample 4 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000379 + Standard deviation subsample 5 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000380 + Standard deviation subsample 6 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000381 + Standard deviation subsample 7 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000382 + Standard deviation subsample 8 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000383 + Standard error subsample 1 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000384 + Standard error subsample 2 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000385 + Standard error subsample 3 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000386 + Standard error subsample 4 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000387 + Standard error subsample 5 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000388 + Standard error subsample 6 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000389 + Standard error subsample 7 + + + + + + + + + jg + 2011-07-22T11:04:09Z + PRIDE + PRIDE:0000390 + Standard error subsample 8 + + + + + + + + jg + 2011-07-26T03:59:31Z + PRIDE + PRIDE:0000391 + Quantification related parameter. + Quantification parameter + + + + + + + + + + + jg + 2011-07-26T04:00:17Z + PRIDE + PRIDE:0000392 + Unit used to report quantification results. + Quantification unit + + + + + + + + + jg + 2011-07-26T04:01:53Z + PRIDE + PRIDE:0000393 + Unit to report relative quantification results. + Relative quantification unit + + + + + + + + + jg + 2011-07-26T04:02:29Z + PRIDE + PRIDE:0000394 + Unit used to describe absolute quantification results. + Absolute quantification unit + + + + + + + + + jg + 2011-07-26T04:12:44Z + PRIDE + PRIDE:0000395 + Quantification results represent ratios. + Ratio + + + + + + + + + jg + 2011-07-26T04:13:32Z + PRIDE + PRIDE:0000396 + Quantification results are reported as copies per cell. + Copies per cell + + + + + + + + + jav + PRIDE + PRIDE:0000397 + One dataset is a reanalysis of previously published data + Data derived from previous dataset + + + + + + + + + jav + PRIDE + PRIDE:0000398 + No post-translational-modifications are been included in the identified peptides of one dataset + No PTMs are included in the dataset + + + + + + + + + jav + PRIDE + PRIDE:0000399 + A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. + Accepted manuscript + + + + + + + + + value-type:xsd:string + PRIDE + PRIDE:0000400 + 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. + Reference + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + PRIDE + PRIDE:0000401 + This means that the experimental information available has been improved, for instance precursor charges were added. + Experimental information has been refined since this experiment was originally made publicly available + + + + + + + + + jav + PRIDE + PRIDE:0000402 + One dataset is not a reanalysis of previously published data + Original data + + + + + + + + + jav + value-type:xsd:string + PRIDE + PRIDE:0000403 + URI of one external file associated to the PRIDE experiment (maybe through a PX submission). + Associated file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + + jav + value-type:xsd:string + PRIDE + PRIDE:0000404 + URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). + Associated raw file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + rc + PRIDE + PRIDE:0000405 + Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission). + Submit PRIDE Experiment to IntAct + + + + + + + + + URI associated to one PX submission in ProteomeCentral. + jav + 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. + jav + 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. + jav + 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. + jav + 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. + jav + 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. + jav + 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. + jav + 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. + jav + 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. + jav + PRIDE + PRIDE:0000414 + Peer-reviewed dataset + + + + + Dataset has been peer-reviewed somehow. + PRIDE:PRIDE + + + + + + + + + Dataset that has not been peer-reviewed by any means. + jav + 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. + jav + 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. + jav + 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. + jav + 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 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 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 + + + + + + + + + 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 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 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 + + + + + + + + + rw + PRIDE + PRIDE:0000425 + MS1 intensity based label-free quantification method + + + + + + + + + acsordas + PRIDE + PRIDE:0000426 + The basic mass spectrometry strategy used in the experiment. + Mass spectrometry proteomics experimental strategy + + + + + + + + + + acsordas + PRIDE + PRIDE:0000427 + Proteins enter directly the mass spectrometer. + Top-down proteomics + + + + + + + + + + acsordas + PRIDE + PRIDE:0000428 + Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer. + Bottom-up proteomics + + + + + + + + + acsordas + PRIDE + PRIDE:0000429 + 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. + MS/MS shotgun proteomics + + + + + + + + + acsordas + PRIDE + PRIDE:0000430 + Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) to provide information about protein folding and protein-protein interaction. + Chemical cross-linking coupled with mass spectrometry proteomics + + + + + + + + + acsordas + PRIDE + PRIDE:0000431 + Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction. + Affinity purification coupled with mass spectrometry proteomics + + + + + + + + + rw + PRIDE + PRIDE:0000432 + A dataset which has an associated manuscript pending for publication. + Dataset with its publication pending + + + + + + + + + acsordas + PRIDE + PRIDE:0000433 + Labeled reagents used for quantification. + Reagents used in Labeled Methods + + + + + + + + + acsordas + PRIDE + PRIDE:0000434 + An unlabeled sample used for quantification. + Unlabeled sample + + + + + + + + + acsordas + PRIDE + PRIDE:0000435 + Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140. + Peptide counting + + + + + + + + + acsordas + PRIDE + PRIDE:0000436 + Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 + Spectrum counting + + + + + + + + + acsordas + PRIDE + PRIDE:0000437 + Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 + Protein Abundance Index - PAI + + + + + + + + + acsordas + PRIDE + PRIDE:0000438 + Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 + Spectrum count/molecular weight + + + + + + + + + acsordas + PRIDE + PRIDE:0000439 + The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 + Spectral Abundance Factor - SAF + + + + + + + + + acsordas + PRIDE + PRIDE:0000440 + Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 + Normalized Spectral Abundance Factor - NSAF + + + + + + + + + acsordas + PRIDE + PRIDE:0000441 + Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 + APEX - Absolute Protein Expression + + + + + + + + + Tissue not applicable to dataset. + rw + 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. + acsordas + 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). + jav + 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). + jav + 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. + jav + 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. + jav + 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 + + + + + + + + + + jav + value-type:xsd:string + PRIDE + PRIDE:0000448 + 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. + Additional associated raw file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + + tt + value-type:xsd:string + PRIDE + PRIDE:0000449 + URI of one gel image file associated to one PX submission. + Gel image file URI + + + + + 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. + acsordas + 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. + acsordas + 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. + acsordas + 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. + acsordas + 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. + acsordas + 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 + + + + + + + + + acsordas + PRIDE + PRIDE:0000455 + Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction. + Protein-protein cross-linking experiment + + + + + + + + + acsordas + PRIDE + PRIDE:0000456 + Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction. + Protein-RNA cross-linking experiment + + + + + + + + PRIDE + PRIDE:0000457 + Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method. + Experiment Type + + + + + + + + + Studying all protein samples of diverse host environments like the human body, soil or sea water. + acsordas + 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 + + + + + + + + + Investigating both human host proteins and associated microbial proteins at the same time from human samples. + acsordas + PRIDE + PRIDE:0000459 + Human Metaproteomics + + + + + Investigating both human host proteins and associated microbial proteins at the same time from human samples. + PRIDE:PRIDE + + + + + + + + + acsordas + PRIDE + PRIDE:0000460 + "Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies." + Proteogenomics + + + + + + + + + Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples. + acsordas + 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. + acsordas + 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 + Parallel Reaction Monitoring (PRM) + + + + + Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. + PRIDE:PRIDE + + + + + + + + + ypriverol + value-type:xsd:string + PRIDE + PRIDE:0000464 + URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission). + Fasta file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + ypriverol + value-type:xsd:string + PRIDE + PRIDE:0000465 + URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission). + Spectral Library file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + ypriverol + value-type:xsd:string + PRIDE + PRIDE:0000466 + URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission). + Quantification result file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + ypriverol + value-type:xsd:string + PRIDE + PRIDE:0000467 + URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission). + MS Image file URI + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + ypriverol + value-type:xsd:string + PRIDE + PRIDE:0000468 + URI for an Aspera Download Protocol + Aspera Protocol + + + + + value-type:xsd:string + The allowed value-type for this CV term. + + + + + + + + + ypriverol + 2018-08-29T14:26:28Z + PRIDE + PRIDE:0000469 + FTP Protocol + + + + + + + + PRIDE File Properties for all type of files. + ypriverol + 2018-08-29T14:26:28Z + PRIDE + PRIDE:0000470 + File Properties + + + + + PRIDE File Properties for all type of files. + PRIDE:PRIDE + + + + + + + + + Properties for MS , Peaks files + ypriverol + 2018-08-29T14:31:06Z + PRIDE + PRIDE:0000471 + MS File Properties + + + + + Properties for MS , Peaks files + PRIDE:PRIDE + + + + + + + + + Minimum charge for all precursor in the file. + ypriverol + 2018-08-29T14:33:01Z + PRIDE + PRIDE:0000472 + MS min charge + + + + + Minimum charge for all precursor in the file. + PRIDE:PRIDE + + + + + + + + + Maximum charge for all precursor in the file. + ypriverol + 2018-08-29T14:35:57Z + PRIDE + PRIDE:0000473 + MS max charge + + + + + Maximum charge for all precursor in the file. + PRIDE:PRIDE + + + + + + + + + Minimum retention time in the File. + ypriverol + 2018-08-29T14:36:50Z + PRIDE + PRIDE:0000474 + MS min RT + + + + + Minimum retention time in the File. + PRIDE:PRIDE + + + + + + + + + Maximum retention time in the file. + ypriverol + 2018-08-29T14:37:30Z + PRIDE + PRIDE:0000475 + MS max RT + + + + + Maximum retention time in the file. + PRIDE:PRIDE + + + + + + + + + Minimum precursor mass to charge in the file. + ypriverol + 2018-08-29T14:38:19Z + PRIDE + PRIDE:0000476 + MS min MZ + + + + + Minimum precursor mass to charge in the file. + PRIDE:PRIDE + + + + + + + + + Maximum precursor mass to charge in the file. + ypriverol + 2018-08-29T14:39:06Z + PRIDE + PRIDE:0000477 + MS max MZ + + + + + Maximum precursor mass to charge in the file. + PRIDE:PRIDE + + + + + + + + + Total number of scans in the file. + ypriverol + 2018-08-29T14:40:05Z + PRIDE + PRIDE:0000478 + Number of scans + + + + + Total number of scans in the file. + PRIDE:PRIDE + + + + + + + + + Range of scan number in the ms file. + ypriverol + 2018-08-29T14:41:09Z + PRIDE + PRIDE:0000479 + MS scan range + + + + + Range of scan number in the ms file. + PRIDE:PRIDE + + + + + + + + + Number of MS in the file. + ypriverol + 2018-08-29T14:43:09Z + PRIDE + PRIDE:0000480 + Number of MS + + + + + Number of MS in the file. + PRIDE:PRIDE + + + + + + + + + Number of MS1 spectra. + ypriverol + 2018-08-29T14:45:21Z + PRIDE + PRIDE:0000481 + Number of MS1 spectra + + + + + Number of MS1 spectra. + PRIDE:PRIDE + + + + + + + + + Number of MS2 spectra in the file. + ypriverol + 2018-08-29T14:46:01Z + PRIDE + PRIDE:0000482 + Number of MS2 spectra + + + + + Number of MS2 spectra in the file. + PRIDE:PRIDE + + + + + + + + + Total number of MS3 spectra in the file. + ypriverol + 2018-08-29T14:48:35Z + 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. + yperez + 2018-09-05T09:08:58Z + 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. + yperez + 2018-09-05T09:11:41Z + PRIDE + PRIDE:0000485 + Global result parameters + + + + + Result analysis parameters share by multiple search engine and Quantiative tools. + PRIDE:PRIDE + + + + + + + + + yperez + 2018-09-05T09:14:02Z + PRIDE + PRIDE:0000486 + Tool specific analysis parameters + + + + + + + + + Minimum charge of precursor to be search. + yperez + 2018-09-05T09:26:36Z + PRIDE + PRIDE:0000487 + Min charge + + + + + Minimum charge of precursor to be search. + PRIDE:PRIDE + + + + + + + + + Maximum charge of precursor to be search. + yperez + 2018-09-05T09:28:29Z + PRIDE + PRIDE:0000488 + Max charge + + + + + Maximum charge of precursor to be search. + PRIDE:PRIDE + + + + + + + + + Min Retention time for precursor to be search. + yperez + 2018-09-05T09:30:51Z + PRIDE + PRIDE:0000489 + Min RT + + + + + Min Retention time for precursor to be search. + PRIDE:PRIDE + + + + + + + + + Maximum precursor RT to be search. + yperez + 2018-09-05T09:31:35Z + PRIDE + PRIDE:0000490 + Max RT + + + + + Maximum precursor RT to be search. + PRIDE:PRIDE + + + + + + + + + Number of missed cleavages. + yperez + 2018-09-05T09:37:09Z + PRIDE + PRIDE:0000491 + Number of missed cleavages + + + + + Number of missed cleavages. + PRIDE:PRIDE + + + + + + + + + Max peptide amino acid length for search. + yperez + 2018-09-05T09:43:03Z + PRIDE + PRIDE:0000492 + Max peptide AA length + + + + + Max peptide amino acid length for search. + PRIDE:PRIDE + + + + + + + + + Minimum peptide amino acid length for search. + yperez + 2018-09-05T09:43:54Z + PRIDE + PRIDE:0000493 + Min peptide AA length + + + + + Minimum peptide amino acid length for search. + PRIDE:PRIDE + + + + + + + + + Min precursor MZ (mass) for precursor to search. + yperez + 2018-09-05T09:47:03Z + PRIDE + PRIDE:0000494 + Min precursor MZ + + + + + Min precursor MZ (mass) for precursor to search. + PRIDE:PRIDE + + + + + + + + + Max precursor MZ (mass) for precursor to search. + yperez + 2018-09-05T09:48:08Z + 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. + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000496 + Min peak length + + + + + Min number of peaks in the spectrum to be search. + PRIDE:PRIDE + + + + + + + + + Use Multi Modification + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000497 + Use Multi Modification + + + + + Use Multi Modification + PRIDE:PRIDE + + + + + + + + + Use Additional Variable Modifications + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000498 + Use Additional Variable Modifications + + + + + Use Additional Variable Modifications + PRIDE:PRIDE + + + + + + + + + Do Mass Filtering + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000499 + Do Mass Filtering + + + + + Do Mass Filtering + PRIDE:PRIDE + + + + + + + + + Intensity Threshold + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000500 + Intensity Threshold + + + + + Intensity Threshold + PRIDE:PRIDE + + + + + + + + + Max Labeled AA + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000501 + Max Labeled AA + + + + + Max Labeled AA + PRIDE:PRIDE + + + + + + + + + Max Number of Modifications (PTMs) + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000502 + Max Number of Modifications (PTMs) + + + + + Max Number of Modifications (PTMs) + PRIDE:PRIDE + + + + + + + + + First Search Precursor Tolerance + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000503 + First Search Precursor Tolerance + + + + + First Search Precursor Tolerance + PRIDE:PRIDE + + + + + + + + + Main Search Precursor Tolerance + yperez + 2018-09-05T10:38:29Z + PRIDE + PRIDE:0000504 + Main Search Precursor Tolerance + + + + + Main Search Precursor Tolerance + PRIDE:PRIDE + + + + + + + + + Accession or Code of the individual in the sample. + yperez + 2018-09-05T10:38:29Z + 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. + yperez + 2019-06-06T13:51:41Z + 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. + yperez + 2019-06-06T13:53:23Z + 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. + yperez + 2019-06-06T13:54:46Z + 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) + yperez + 2019-06-06T13:56:00Z + PRIDE + PRIDE:0000509 + Number of PSMs + + + + + Total number of reported identified Peptide Spectrum matches (PSMs) + PRIDE:PRIDE + + + + + + + + + The size of the file in MB. + mwalzer + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000510 + File size + + + + + The size of the file in MB. + PRIDE:PRIDE + + + + + + + + + Pass submitter threshold + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000511 + Pass submitter threshold + + + + + Pass submitter threshold + PRIDE:PRIDE + + + + + + + + + RNA mass spectrometry + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000512 + RNA mass spectrometry + + + + + RNA mass spectrometry + PRIDE:PRIDE + + + + + + + + + Dimethyl Labeling (DML) + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000513 + Dimethyl Labeling + + + + + Dimethyl Labeling (DML) + PRIDE:PRIDE + + + + + + + + + Quantification channel label + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000514 + Label + + + + + Quantification channel label + PRIDE:PRIDE + + + + + + + + + TMT + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000515 + TMT + + + + + TMT + PRIDE:PRIDE + + + + + + + + + TMT126 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000516 + TMT126 + + + + + TMT126 + PRIDE:PRIDE + + + + + + + + + TMT127 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000517 + TMT127 + + + + + TMT127 + PRIDE:PRIDE + + + + + + + + + TMT127C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000518 + TMT127C + + + + + TMT127C + PRIDE:PRIDE + + + + + + + + + TMT127N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000519 + TMT127N + + + + + TMT127N + PRIDE:PRIDE + + + + + + + + + TMT128 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000520 + TMT128 + + + + + TMT128 + PRIDE:PRIDE + + + + + + + + + TMT128C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000521 + TMT128C + + + + + TMT128C + PRIDE:PRIDE + + + + + + + + + TMT128N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000522 + TMT128N + + + + + TMT128N + PRIDE:PRIDE + + + + + + + + + TMT129 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000523 + TMT129 + + + + + TMT129 + PRIDE:PRIDE + + + + + + + + + TMT129C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000524 + TMT129C + + + + + TMT129C + PRIDE:PRIDE + + + + + + + + + TMT129N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000525 + TMT129N + + + + + TMT129N + PRIDE:PRIDE + + + + + + + + + TMT130 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000526 + TMT130 + + + + + TMT130 + PRIDE:PRIDE + + + + + + + + + TMT130C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000527 + TMT130C + + + + + TMT130C + PRIDE:PRIDE + + + + + + + + + TMT130N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000528 + TMT130N + + + + + TMT130N + PRIDE:PRIDE + + + + + + + + + TMT131 + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000529 + TMT131 + + + + + TMT131 + PRIDE:PRIDE + + + + + + + + + ITRAQ channel label + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000530 + ITRAQ + + + + + ITRAQ channel label + PRIDE:PRIDE + + + + + + + + + yperez + 2020-03-16T18:02:43Z + PRIDE + PRIDE:0000531 + ITRAQ113 + + + + + + + + + yperez + 2020-03-16T18:03:15Z + PRIDE + PRIDE:0000532 + ITRAQ114 + + + + + + + + + yperez + 2020-03-16T18:03:31Z + PRIDE + PRIDE:0000533 + ITRAQ115 + + + + + + + + + yperez + 2020-03-16T18:03:49Z + PRIDE + PRIDE:0000534 + ITRAQ116 + + + + + + + + + yperez + 2020-03-16T18:04:10Z + PRIDE + PRIDE:0000535 + ITRAQ117 + + + + + + + + + yperez + 2020-03-16T18:04:30Z + PRIDE + PRIDE:0000536 + ITRAQ118 + + + + + + + + + yperez + 2020-03-16T18:04:49Z + PRIDE + PRIDE:0000537 + ITRAQ119 + + + + + + + + + yperez + 2020-03-16T18:05:06Z + PRIDE + PRIDE:0000538 + ITRAQ121 + + + + + + + + + SILAC channel label + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000539 + SILAC + + + + + SILAC channel label + PRIDE:PRIDE + + + + + + + + + ICAT channel label + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000540 + ICAT + + + + + ICAT channel label + PRIDE:PRIDE + + + + + + + + + ICAT heavy + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000541 + ICAT heavy + + + + + ICAT heavy + PRIDE:PRIDE + + + + + + + + + ICAT light + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000542 + ICAT light + + + + + ICAT light + PRIDE:PRIDE + + + + + + + + + MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring. + PRIDE + PRIDE:0000543 + Example description of such experiments in 10.1002/pmic.201000578 + Quality Control + + + + + MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring. + 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 + Example description of such samples in 10.1002/pmic.201000578 + 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 + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000547 + Instrument properties + + + + + Instrument properties + PRIDE:PRIDE + + + + + + + + + MS1 mass analyzer + yperez + 2020-03-16T18:01:06Z + PRIDE + PRIDE:0000548 + MS1 mass analyzer + + + + + MS1 mass analyzer + PRIDE:PRIDE + + + + + + + + + MS2 mass analyzer + yperez + 2020-03-16T18:01:06Z + 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 fractionation methods. + PRIDE + PRIDE:0000551 + Separation method + + + + + Umbrella term for different types of fractionation 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 + + + + + + + + + Indicates that this protein identification comes from the used decoy database. + yperez + 2020-05-12T11:58:52Z + PRIDE + PRIDE:0000570 + Decoy protein + + + + + Indicates that this protein identification comes from the used decoy database. + PRIDE:PRIDE + + + + + + + + A software that perform protein quantification using mass spectrometry data. + yperez + 2020-05-12T11:58:52Z + 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. + yperez + 2020-05-12T11:58:52Z + 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. + yperez + 2020-05-12T11:58:52Z + 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. + yperez + 2020-05-12T11:58:52Z + 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 + yperez + 2020-05-12T11:58:52Z + 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 + yperez + 2020-05-12T11:58:52Z + 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 (maybe through a PX submission) + yperez + 2020-05-12T11:58:52Z + PRIDE + PRIDE:0000577 + file uri + + + + + URI of one external file associated to the PRIDE experiment (maybe through a PX submission) + PRIDE:PRIDE + + + + + + + + + The bound fraction after a depletion process + lisavetasol + PRIDE + PRIDE:0000578 + Bound fraction + + + + + The bound fraction after a depletion process + PRIDE:PRIDE + + + + + + + + + The depleted fraction after a depletion process + lisavetasol + PRIDE + PRIDE:0000579 + Depleted fraction + + + + + The depleted fraction after a depletion process + PRIDE:PRIDE + + + + + + + + + TMT131N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000580 + TMT131N + + + + + TMT131N + PRIDE:PRIDE + + + + + + + + + TMT131C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000581 + TMT131C + + + + + TMT131C + PRIDE:PRIDE + + + + + + + + + TMT132N + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000582 + TMT132N + + + + + TMT132N + PRIDE:PRIDE + + + + + + + + + TMT132C + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000583 + TMT132C + + + + + TMT132C + PRIDE:PRIDE + + + + + + + + + + Experimental design file URI + yperez + 2019-08-07T15:21:19Z + 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 + + + + + + + + + + + + + + + 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 + yperez + 2020-05-12T11:58:52Z + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + 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 + lisavetasol + PRIDE + PRIDE:0000610 + Beta-mercaptoethanol (BME) + + + + + The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS + PRIDE:PRIDE + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000611 + The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4) + SILAC light R:12C(6)14N(4) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000612 + The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6) + SILAC light L:12C(6) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000613 + The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2) + SILAC light K:12C(6)14N(2) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000614 + The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5) + SILAC light P:12C(5) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000615 + The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4) + SILAC heavy R:13C(6)15N(4) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000616 + The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6) + SILAC heavy L:13C(6) + + + + + + + + + yperez + 2011-07-22T09:45:40Z + PRIDE + PRIDE:0000617 + The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2) + SILAC heavy K:13C(6)15N(2) + + + + + + + + + yperez + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000618 + The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4). + SILAC medium R:13C(6)14N(4) + + + + + + + + + yperez + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000619 + The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2). + SILAC medium K:13C(6)14N(2) + + + + + + + + + yperez + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000620 + Metabolic label 15N + 15N + + + + + + + + + yperez + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000621 + Metabolic label 13C + 13C + + + + + + + + + yperez + 2011-07-22T09:47:09Z + PRIDE + PRIDE:0000622 + Metabolic label 18O + 18O + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000623 + Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics + original source name + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000624 + Spectra Cluster Maximum Ratio for the cluster + SpectraCluster MaxRatio + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000625 + NIST Probability Correlation + NIST ProbCorr + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000626 + NIST best dot product + NIST Dotbest + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000627 + Data-dependent acquisition + Data-dependent acquisition + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000629 + Parallel Reaction Monitoring (PRM) + Parallel reaction monitoring + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000630 + Selected reaction monitoring (SRM) + Selected reaction monitoring + + + + + + + + + yperez + 2020-23-22T09:47:09Z + PRIDE + PRIDE:0000631 + Mass spectrometry imaging + Mass spectrometry imaging + + + + + + + + + TMT133N + yperez + 2022-08-07T15:21:19Z + PRIDE + PRIDE:0000632 + TMT133N + + + + + TMT133N + PRIDE:PRIDE + + + + + + + + + TMT133C + yperez + 2022-08-07T15:21:19Z + PRIDE + PRIDE:0000633 + TMT133C + + + + + TMT133C + PRIDE:PRIDE + + + + + + + + + TMT134N + yperez + 2022-08-07T15:21:19Z + PRIDE + PRIDE:0000634 + TMT134N + + + + + TMT134N + PRIDE:PRIDE + + + + + + + + + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000635 + The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes. + Affinity proteomics + + + + + + + + + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000636 + 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. + SomaScan affinity proteomics + + + + + + + + + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000637 + 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. + Olink affinity proteomics + + + + + + + + Instrument model + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000638 + Instrument model + + + + + Instrument model + PRIDE:PRIDE + + + + + + + + + Somalogic instrument model + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000639 + Somalogic instrument model + + + + + Somalogic instrument model + PRIDE:PRIDE + + + + + + + + + SomaScan assay v4.0 + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000640 + SomaScan assay v4.0 + + + + + SomaScan assay v4.0 + PRIDE:PRIDE + + + + + + + + + SomaScan assay v4.1 + yperez + 2023-08-05T15:21:19Z + PRIDE + PRIDE:0000641 + SomaScan assay v4.1 + + + + + SomaScan assay v4.1 + PRIDE:PRIDE + + + + + + + + + TMT134C + Roman-Si + 2023-10-05T11:44:19Z + PRIDE + PRIDE:0000642 + TMT134C + + + + + TMT134C + PRIDE:PRIDE + + + + + + + + + TMT135N + Roman-Si + 2023-10-05T11:44:19Z + PRIDE + PRIDE:0000643 + TMT135N + + + + + TMT135N + PRIDE:PRIDE + + + + + + + + + Fragmentation method used for dissociation or fragmentation for MS2 + yperez + 2023-10-12T11:44:19Z + 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 + yperez + 2023-10-12T11:44:19Z + PRIDE + PRIDE:0000645 + MS3 dissociation method + + + + + Fragmentation method used for dissociation or fragmentation for MS3 + PRIDE:PRIDE + + + + + + + + + MS3 mass analyzer + yperez + 2023-10-12T18:01:06Z + PRIDE + PRIDE:0000646 + MS3 mass analyzer + + + + + MS3 mass analyzer + PRIDE:PRIDE + + + + + + +