OBO-Edit 2.3.1 12:11:2024 11:31 PRIDE 1.4 Deepti Jaiswal Kundu 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 PRIDE MS:1000451 mass analyzer mass analyzer PRIDE:PRIDE A sample that has not been labelled or modified PRIDE MS:1002038 label free sample A sample that has not been labelled or modified PRIDE:PRIDE The date on which data creation began [NCI] 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: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. PRIDE PRIDE:0000300 Gel spot identifier The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication. PRIDE:PRIDE Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value). PRIDE PRIDE:0000301 Non-significant protein identification Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value). PRIDE:PRIDE Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value). PRIDE PRIDE:0000302 Non-significant peptide identification Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value). PRIDE:PRIDE Indicates that this protein identification comes from the used decoy database. PRIDE PRIDE:0000303 Decoy hit 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. PRIDE PRIDE:0000304 Gel identifier The gel's identifier. This identifier should resemble the one used in, for example, the associated publication. PRIDE:PRIDE Defines a gel-based proteomics experiment. PRIDE PRIDE:0000305 Gel-based experiment Defines a gel-based proteomics experiment. PRIDE:PRIDE PRIDE PRIDE:0000306 Experiment.[Curator:ACSORDAS] Imported from NCBI Peptidome PRIDE PRIDE:0000307 Defines various quantification methods Quantification method PRIDE PRIDE:0000308 Describes gel-based quantification methods Gel-based quantification method PRIDE PRIDE:0000309 Describes gel-free quantification methods Gel-free quantification method PRIDE PRIDE:0000310 Describes quantification techniques using isotope labeling Isotope labeling PRIDE PRIDE:0000311 Describes quantification techniques based on selected / multiple reaction monitoring Selected Reaction Monitoring PRIDE PRIDE:0000312 Describes label free quantification techniques. Label free PRIDE PRIDE:0000313 Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level iTRAQ Tandem Mass Tag PRIDE PRIDE:0000314 Tandem Mass Tag is a MS2 based isotope labeling quantification technique TMT 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 PRIDE PRIDE:0000316 Describes isotope labeling quantification techniques detectable at MS1 level. MS1 based isotope labeling PRIDE PRIDE:0000317 Describes isotope labeling quantification techniques detectable at MS1 level. MS2 based isotope labeling PRIDE PRIDE:0000318 The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. 18O 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 PRIDE PRIDE:0000320 AQUA is an isotope labeling based quantification technique that uses known peptides. AQUA 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 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 Total Ion Current PRIDE PRIDE:0000323 The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. TIC PRIDE PRIDE:0000324 A reagent used for quantification. Quantification reagent PRIDE PRIDE:0000325 The heavy label used in SILAC experiments. SILAC heavy PRIDE PRIDE:0000326 The light reagent used in SILAC experiments. SILAC light PRIDE PRIDE:0000327 The medium weight reagent used in SILAC experiments. SILAC medium PRIDE PRIDE:0000328 Reagent used in SILAC labeling. SILAC reagent PRIDE PRIDE:0000329 Reagent used in iTRAQ experiments. iTRAQ reagent 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 PRIDE PRIDE:0000331 Quantification values reported as arbitrary counts (most often ion counts). Counts PRIDE PRIDE:0000337 Reagent used in TMT experiments. TMT reagent PRIDE PRIDE:0000344 Reagent used in ICAT experiments. ICAT reagent PRIDE PRIDE:0000345 ICAT light reagent PRIDE PRIDE:0000346 ICAT heavy reagent PRIDE PRIDE:0000347 Reagent used in ICPL experiments. ICPL reagent PRIDE PRIDE:0000348 ICPL 0 reagent PRIDE PRIDE:0000349 ICPL 4 reagent PRIDE PRIDE:0000350 ICPL 6 reagent PRIDE PRIDE:0000351 ICPL 10 reagent PRIDE PRIDE:0000352 Parameters to report quantification values. Quantification value PRIDE PRIDE:0000353 Parameters describing quantification values for multiplexed samples. Multiplexed quantification value PRIDE PRIDE:0000354 Intensity subsample 1 PRIDE PRIDE:0000355 Intensity subsample 2 PRIDE PRIDE:0000356 Intensity subsample 3 PRIDE PRIDE:0000357 Intensity subsample 4 PRIDE PRIDE:0000358 Intensity subsample 5 PRIDE PRIDE:0000359 Intensity subsample 6 PRIDE PRIDE:0000360 Intensity subsample 7 PRIDE PRIDE:0000361 Intensity subsample 8 PRIDE PRIDE:0000362 Values from other quantification techniques. Other quantification value PRIDE PRIDE:0000363 The emPAI for the protein. emPAI value PRIDE PRIDE:0000364 The Total Ion Count for the given entity. TIC value PRIDE PRIDE:0000365 Describes multiples subsamples. Multiplexed sample description PRIDE PRIDE:0000366 Identifies samples that are made up of multiplexed subsamples. Contains multiple subsamples PRIDE PRIDE:0000367 Subsample 1 description PRIDE PRIDE:0000368 Subsample 2 description PRIDE PRIDE:0000369 Subsample 3 description PRIDE PRIDE:0000370 Subsample 4 description PRIDE PRIDE:0000371 Subsample 5 description PRIDE PRIDE:0000372 Subsample 6 description PRIDE PRIDE:0000373 Subsample 7 description PRIDE PRIDE:0000374 Subsample 8 description PRIDE PRIDE:0000375 Standard deviation subsample 1 PRIDE PRIDE:0000376 Standard deviation subsample 2 PRIDE PRIDE:0000377 Standard deviation subsample 3 PRIDE PRIDE:0000378 Standard deviation subsample 4 PRIDE PRIDE:0000379 Standard deviation subsample 5 PRIDE PRIDE:0000380 Standard deviation subsample 6 PRIDE PRIDE:0000381 Standard deviation subsample 7 PRIDE PRIDE:0000382 Standard deviation subsample 8 PRIDE PRIDE:0000383 Standard error subsample 1 PRIDE PRIDE:0000384 Standard error subsample 2 PRIDE PRIDE:0000385 Standard error subsample 3 PRIDE PRIDE:0000386 Standard error subsample 4 PRIDE PRIDE:0000387 Standard error subsample 5 PRIDE PRIDE:0000388 Standard error subsample 6 PRIDE PRIDE:0000389 Standard error subsample 7 PRIDE PRIDE:0000390 Standard error subsample 8 PRIDE PRIDE:0000391 Quantification related parameter. Quantification parameter PRIDE PRIDE:0000392 Unit used to report quantification results. Quantification unit PRIDE PRIDE:0000393 Unit to report relative quantification results. Relative quantification unit PRIDE PRIDE:0000394 Unit used to describe absolute quantification results. Absolute quantification unit PRIDE PRIDE:0000395 Quantification results represent ratios. Ratio PRIDE PRIDE:0000396 Quantification results are reported as copies per cell. Copies per cell PRIDE PRIDE:0000397 One dataset is a reanalysis of previously published data Data derived from previous dataset PRIDE PRIDE:0000398 No post-translational-modifications are been included in the identified peptides of one dataset No PTMs are included in the dataset 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 PRIDE PRIDE:0000402 One dataset is not a reanalysis of previously published data Original data 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. 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. 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. value-type:xsd:string PRIDE PRIDE:0000406 ProteomeCentral dataset URI URI associated to one PX submission in ProteomeCentral. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. URI of one file labeled as 'Result', associated to one PX submission. value-type:xsd:string PRIDE PRIDE:0000407 Result file URI URI of one file labeled as 'Result', associated to one PX submission. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. URI of one search engine output file associated to one PX submission. value-type:xsd:string PRIDE PRIDE:0000408 Search engine output file URI URI of one search engine output file associated to one PX submission. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. URI of one of one search engine output file associated to one PX submission. value-type:xsd:string PRIDE PRIDE:0000409 Peak list file URI URI of one of one search engine output file associated to one PX submission. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. URI of one file labeled as 'Other', associated to one PX submission. value-type:xsd:string PRIDE PRIDE:0000410 'Other' type file URI URI of one file labeled as 'Other', associated to one PX submission. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. FTP location of one entire PX data set. value-type:xsd:string PRIDE PRIDE:0000411 Dataset FTP location FTP location of one entire PX data set. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. A dataset which does not have an associated published manuscript. PRIDE PRIDE:0000412 Dataset with no associated published manuscript A dataset which does not have an associated published manuscript. PRIDE:PRIDE The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet. value-type:xsd:string PRIDE PRIDE:0000413 Instrument name The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet. PRIDE:PRIDE value-type:xsd:string The allowed value-type for this CV term. Dataset has been peer-reviewed somehow. PRIDE PRIDE:0000414 Peer-reviewed dataset Dataset has been peer-reviewed somehow. PRIDE:PRIDE Dataset that has not been peer-reviewed by any means. PRIDE PRIDE:0000415 Non peer-reviewed dataset Dataset that has not been peer-reviewed by any means. PRIDE:PRIDE The PX dataset is supported by and is available through the submission repository. PRIDE PRIDE:0000416 Supported dataset by repository The PX dataset is supported by and is available through the submission repository. PRIDE:PRIDE The PX dataset is not fully supported by the submission repository. PRIDE PRIDE:0000417 Unsupported dataset by repository The PX dataset is not fully supported by the submission repository. PRIDE:PRIDE Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself. PRIDE PRIDE:0000418 Other member of protein ambiguity group Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself. PRIDE:PRIDE B ion type with a neutral loss of a phosphate molecule. b fragment ion -H3PO4 PRIDE PRIDE:0000419 b ion -H3PO4 B ion type with a neutral loss of a phosphate molecule. PRIDE:PRIDE B 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 PRIDE PRIDE:0000425 MS1 intensity based label-free quantification method PRIDE PRIDE:0000426 The basic mass spectrometry strategy used in the experiment. Mass spectrometry proteomics experimental strategy PRIDE PRIDE:0000427 Proteins enter directly the mass spectrometer. Top-down proteomics PRIDE PRIDE:0000428 Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer. Bottom-up proteomics 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 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 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 PRIDE PRIDE:0000432 A dataset which has an associated manuscript pending for publication. Dataset with its publication pending PRIDE PRIDE:0000433 Labeled reagents used for quantification. Reagents used in Labeled Methods PRIDE PRIDE:0000434 An unlabeled sample used for quantification. Unlabeled sample 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 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 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 PAI PRIDE PRIDE:0000438 Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 Spectrum count/molecular weight PRIDE PRIDE:0000439 The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 SAF PRIDE PRIDE:0000440 Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 NSAF 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. PRIDE PRIDE:0000442 Tissue not applicable to dataset Tissue not applicable to dataset. PRIDE:PRIDE The NCBI FTP location of the original Sample - Experiment level Peptidome submission data. PRIDE PRIDE:0000443 Original NCBI Peptidome submission files The NCBI FTP location of the original Sample - Experiment level Peptidome submission data. PRIDE:PRIDE Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system). PRIDE PRIDE:0000444 PRIDE experiment accession Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system). PRIDE:PRIDE It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc). PRIDE PRIDE:0000445 PRIDE Cluster score It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc). PRIDE:PRIDE Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243. PRIDE PRIDE:0000446 PRIDE peptide score Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243. PRIDE:PRIDE ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725. PRIDE PRIDE:0000447 SWATH MS ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725. PRIDE:PRIDE 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. 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. PRIDE PRIDE:0000450 Data-independent acquisition Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846. PRIDE:PRIDE Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610. PRIDE PRIDE:0000451 MSE Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610. PRIDE:PRIDE Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061. PRIDE PRIDE:0000452 HDMSE Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061. PRIDE:PRIDE Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720. PRIDE PRIDE:0000453 PAcIFIC Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720. PRIDE:PRIDE MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777. PRIDE PRIDE:0000454 All-ion fragmentation MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777. PRIDE:PRIDE PRIDE PRIDE:0000455 Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction. Protein-protein cross-linking experiment 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. 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. PRIDE PRIDE:0000459 Human Metaproteomics Investigating both human host proteins and associated microbial proteins at the same time from human samples. PRIDE:PRIDE 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. PRIDE PRIDE:0000461 Multi-omics study Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples. PRIDE:PRIDE Waters data independent acquisition method. PRIDE PRIDE:0000462 SONAR Waters data independent acquisition method. PRIDE:PRIDE Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. PRIDE PRIDE:0000463 PRM Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. PRIDE:PRIDE 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. 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. 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. 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. 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. PRIDE PRIDE:0000469 FTP Protocol PRIDE File Properties for all type of files. PRIDE PRIDE:0000470 File Properties PRIDE File Properties for all type of files. PRIDE:PRIDE Properties for MS , Peaks files PRIDE PRIDE:0000471 MS File Properties Properties for MS , Peaks files PRIDE:PRIDE Minimum charge for all precursor in the file. PRIDE PRIDE:0000472 MS min charge Minimum charge for all precursor in the file. PRIDE:PRIDE Maximum charge for all precursor in the file. PRIDE PRIDE:0000473 MS max charge Maximum charge for all precursor in the file. PRIDE:PRIDE Minimum retention time in the File. PRIDE PRIDE:0000474 MS min RT Minimum retention time in the File. PRIDE:PRIDE Maximum retention time in the file. PRIDE PRIDE:0000475 MS max RT Maximum retention time in the file. PRIDE:PRIDE Minimum precursor mass to charge in the file. PRIDE PRIDE:0000476 MS min MZ Minimum precursor mass to charge in the file. PRIDE:PRIDE Maximum precursor mass to charge in the file. PRIDE PRIDE:0000477 MS max MZ Maximum precursor mass to charge in the file. PRIDE:PRIDE Total number of scans in the file. PRIDE PRIDE:0000478 Number of scans Total number of scans in the file. PRIDE:PRIDE Range of scan number in the ms file. PRIDE PRIDE:0000479 MS scan range Range of scan number in the ms file. PRIDE:PRIDE Number of MS in the file. PRIDE PRIDE:0000480 Number of MS Number of MS in the file. PRIDE:PRIDE Number of MS1 spectra. PRIDE PRIDE:0000481 Number of MS1 spectra Number of MS1 spectra. PRIDE:PRIDE Number of MS2 spectra in the file. PRIDE PRIDE:0000482 Number of MS2 spectra Number of MS2 spectra in the file. PRIDE:PRIDE Total number of MS3 spectra in the file. PRIDE PRIDE:0000483 Number of MS3 spectra Total number of MS3 spectra in the file. PRIDE:PRIDE The result analysis parameters is a term to group all the parameters for proteomics data analysis. PRIDE PRIDE:0000484 Result analysis parameters The result analysis parameters is a term to group all the parameters for proteomics data analysis. PRIDE:PRIDE Result analysis parameters share by multiple search engine and Quantiative tools. PRIDE PRIDE:0000485 Global result parameters Result analysis parameters share by multiple search engine and Quantiative tools. PRIDE:PRIDE PRIDE PRIDE:0000486 Tool specific analysis parameters Minimum charge of precursor to be search. PRIDE PRIDE:0000487 Min charge Minimum charge of precursor to be search. PRIDE:PRIDE Maximum charge of precursor to be search. PRIDE PRIDE:0000488 Max charge Maximum charge of precursor to be search. PRIDE:PRIDE Min Retention time for precursor to be search. PRIDE PRIDE:0000489 Min RT Min Retention time for precursor to be search. PRIDE:PRIDE Maximum precursor RT to be search. PRIDE PRIDE:0000490 Max RT Maximum precursor RT to be search. PRIDE:PRIDE Number of missed cleavages. PRIDE PRIDE:0000491 Number of missed cleavages Number of missed cleavages. PRIDE:PRIDE Max peptide amino acid length for search. PRIDE PRIDE:0000492 Max peptide AA length Max peptide amino acid length for search. PRIDE:PRIDE Minimum peptide amino acid length for search. PRIDE PRIDE:0000493 Min peptide AA length Minimum peptide amino acid length for search. PRIDE:PRIDE Min precursor MZ (mass) for precursor to search. PRIDE PRIDE:0000494 Min precursor MZ Min precursor MZ (mass) for precursor to search. PRIDE:PRIDE Max precursor MZ (mass) for precursor to search. PRIDE PRIDE:0000495 Max precursor MZ Max precursor MZ (mass) for precursor to search. PRIDE:PRIDE Min number of peaks in the spectrum to be search. PRIDE PRIDE:0000496 Min peak length Min number of peaks in the spectrum to be search. PRIDE:PRIDE Use Multi Modification PRIDE PRIDE:0000497 Use Multi Modification Use Multi Modification PRIDE:PRIDE Use Additional Variable Modifications PRIDE PRIDE:0000498 Use Additional Variable Modifications Use Additional Variable Modifications PRIDE:PRIDE Do Mass Filtering PRIDE PRIDE:0000499 Do Mass Filtering Do Mass Filtering PRIDE:PRIDE Intensity Threshold PRIDE PRIDE:0000500 Intensity Threshold Intensity Threshold PRIDE:PRIDE Max Labeled AA PRIDE PRIDE:0000501 Max Labeled AA Max Labeled AA PRIDE:PRIDE Max Number of Modifications (PTMs) PRIDE PRIDE:0000502 Max Number of Modifications (PTMs) Max Number of Modifications (PTMs) PRIDE:PRIDE First Search Precursor Tolerance PRIDE PRIDE:0000503 First Search Precursor Tolerance First Search Precursor Tolerance PRIDE:PRIDE Main Search Precursor Tolerance PRIDE PRIDE:0000504 Main Search Precursor Tolerance Main Search Precursor Tolerance PRIDE:PRIDE Accession or Code of the individual in the sample. PRIDE PRIDE:0000505 Individual Accession Accession or Code of the individual in the sample. PRIDE:PRIDE Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment. PRIDE PRIDE:0000506 Number identified proteins Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment. PRIDE:PRIDE Total number of identified peptides in an experiment or assay. PRIDE PRIDE:0000507 Number of identified peptides Total number of identified peptides in an experiment or assay. PRIDE:PRIDE The total number of peptides identified with post-translational modifications. PRIDE PRIDE:0000508 Number of modified peptides The total number of peptides identified with post-translational modifications. PRIDE:PRIDE Total number of reported identified Peptide Spectrum matches (PSMs) PRIDE PRIDE:0000509 Number of PSMs Total number of reported identified Peptide Spectrum matches (PSMs) PRIDE:PRIDE The size of the file in MB. PRIDE PRIDE:0000510 File size The size of the file in MB. PRIDE:PRIDE Pass submitter threshold PRIDE PRIDE:0000511 Pass submitter threshold Pass submitter threshold PRIDE:PRIDE RNA mass spectrometry PRIDE PRIDE:0000512 RNA mass spectrometry RNA mass spectrometry PRIDE:PRIDE Dimethyl Labeling (DML) PRIDE PRIDE:0000513 Dimethyl Labeling Dimethyl Labeling (DML) PRIDE:PRIDE Quantification channel label PRIDE PRIDE:0000514 Label Quantification channel label PRIDE:PRIDE TMT PRIDE PRIDE:0000515 TMT TMT PRIDE:PRIDE TMT126 PRIDE PRIDE:0000516 TMT126 TMT126 PRIDE:PRIDE TMT127 PRIDE PRIDE:0000517 TMT127 TMT127 PRIDE:PRIDE TMT127C PRIDE PRIDE:0000518 TMT127C TMT127C PRIDE:PRIDE TMT127N PRIDE PRIDE:0000519 TMT127N TMT127N PRIDE:PRIDE TMT128 PRIDE PRIDE:0000520 TMT128 TMT128 PRIDE:PRIDE TMT128C PRIDE PRIDE:0000521 TMT128C TMT128C PRIDE:PRIDE TMT128N PRIDE PRIDE:0000522 TMT128N TMT128N PRIDE:PRIDE TMT129 PRIDE PRIDE:0000523 TMT129 TMT129 PRIDE:PRIDE TMT129C PRIDE PRIDE:0000524 TMT129C TMT129C PRIDE:PRIDE TMT129N PRIDE PRIDE:0000525 TMT129N TMT129N PRIDE:PRIDE TMT130 PRIDE PRIDE:0000526 TMT130 TMT130 PRIDE:PRIDE TMT130C PRIDE PRIDE:0000527 TMT130C TMT130C PRIDE:PRIDE TMT130N PRIDE PRIDE:0000528 TMT130N TMT130N PRIDE:PRIDE TMT131 PRIDE PRIDE:0000529 TMT131 TMT131 PRIDE:PRIDE ITRAQ channel label PRIDE PRIDE:0000530 ITRAQ ITRAQ channel label PRIDE:PRIDE PRIDE PRIDE:0000531 ITRAQ113 PRIDE PRIDE:0000532 ITRAQ114 PRIDE PRIDE:0000533 ITRAQ115 PRIDE PRIDE:0000534 ITRAQ116 PRIDE PRIDE:0000535 ITRAQ117 PRIDE PRIDE:0000536 ITRAQ118 PRIDE PRIDE:0000537 ITRAQ119 PRIDE PRIDE:0000538 ITRAQ121 SILAC channel label PRIDE PRIDE:0000539 SILAC SILAC channel label PRIDE:PRIDE ICAT channel label PRIDE PRIDE:0000540 ICAT ICAT channel label PRIDE:PRIDE ICAT heavy PRIDE PRIDE:0000541 ICAT heavy ICAT heavy PRIDE:PRIDE ICAT light PRIDE PRIDE:0000542 ICAT light ICAT light PRIDE:PRIDE MS experiments conducted to control the quality of measurements. 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 PRIDE PRIDE:0000547 Instrument properties Instrument properties PRIDE:PRIDE MS1 mass analyzer PRIDE PRIDE:0000548 MS1 mass analyzer MS1 mass analyzer PRIDE:PRIDE MS2 mass analyzer PRIDE PRIDE:0000549 MS2 mass analyzer MS2 mass analyzer PRIDE:PRIDE Umbrella term for different types of fractionation methods. PRIDE PRIDE:0000550 Fractionation method Umbrella term for different types of fractionation methods. PRIDE:PRIDE Umbrella term for different types of 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. 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. PRIDE PRIDE:0000571 Quantification software A software that perform protein quantification using mass spectrometry data. PRIDE:PRIDE OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. PRIDE PRIDE:0000572 OpenMS OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. PRIDE:PRIDE A software that perform peptide/protein identification using mass spectrometry data. 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. PRIDE PRIDE:0000574 MaxQuant MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. PRIDE:PRIDE Threshold at precursor level to compare experimental mass with theoretical mass PRIDE PRIDE:0000575 precursor mass tolerance Threshold at precursor level to compare experimental mass with theoretical mass PRIDE:PRIDE Threshold at fragment level to compare experimental mass with theoretical mass PRIDE PRIDE:0000576 fragment mass tolerance Threshold at fragment level to compare experimental mass with theoretical mass PRIDE:PRIDE URI of one external file associated to the PRIDE experiment (maybe through a PX submission) 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 PRIDE PRIDE:0000578 Bound fraction The bound fraction after a depletion process PRIDE:PRIDE The depleted fraction after a depletion process PRIDE PRIDE:0000579 Depleted fraction The depleted fraction after a depletion process PRIDE:PRIDE TMT131N PRIDE PRIDE:0000580 TMT131N TMT131N PRIDE:PRIDE TMT131C PRIDE PRIDE:0000581 TMT131C TMT131C PRIDE:PRIDE TMT132N PRIDE PRIDE:0000582 TMT132N TMT132N PRIDE:PRIDE TMT132C PRIDE PRIDE:0000583 TMT132C TMT132C PRIDE:PRIDE Experimental design file URI PRIDE PRIDE:0000584 Experimental design file URI Experimental design file URI PRIDE:PRIDE Enrichment of specific post-translational modifications PRIDE PRIDE:0000585 Enrichment Enrichment of specific post-translational modifications PRIDE:PRIDE Enrichment method Enrichment of specific post-translational modifications PRIDE PRIDE:0000586 Enrichment method Enrichment method Enrichment of specific post-translational modifications PRIDE:PRIDE The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides PRIDE PRIDE:0000587 IMAC The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides PRIDE:PRIDE Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples PRIDE PRIDE:0000588 TIO2 Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples PRIDE:PRIDE A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy). PRIDE PRIDE:0000589 EThcD A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy). PRIDE:PRIDE beam-type collision-induced dissociation PRIDE PRIDE:0000590 HCD beam-type collision-induced dissociation PRIDE:PRIDE collision-induced dissociation PRIDE PRIDE:0000591 CID collision-induced dissociation PRIDE:PRIDE ETD with supplemental activation ETcaD PRIDE PRIDE:0000592 ETciD ETD with supplemental activation PRIDE:PRIDE CID collision energy PRIDE PRIDE:0000593 CID collision energy CID collision energy PRIDE:PRIDE HCD collision energy PRIDE PRIDE:0000594 HCD collision energy HCD collision energy PRIDE:PRIDE EThcD collision energy PRIDE PRIDE:0000595 EThcD collision energy EThcD collision energy PRIDE:PRIDE ETciD collision energy PRIDE PRIDE:0000596 ETciD collision energy ETciD collision energy PRIDE:PRIDE metabolic label PRIDE PRIDE:0000597 metabolic label metabolic label PRIDE:PRIDE The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds PRIDE PRIDE:0000598 Alkylation reagent The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds PRIDE:PRIDE The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE PRIDE:0000599 Iodoacetamide (IAA) The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE:PRIDE The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE PRIDE:0000600 Chloroacetamide (ClAA) The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da PRIDE:PRIDE The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE PRIDE:0000601 Iodoacetic acid (IAC) The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE:PRIDE The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE PRIDE:0000602 Chloroacetic acid (ClAC) The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da PRIDE:PRIDE The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da PRIDE PRIDE:0000603 Acrylamide (AA) The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da PRIDE:PRIDE The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da PRIDE PRIDE:0000604 4-Vinylpyridine (4-VP) The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da PRIDE:PRIDE The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da PRIDE PRIDE:0000605 Methyl methanethiosulfonate (MMTS) The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da PRIDE:PRIDE The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da PRIDE PRIDE:0000606 N-ethylmaleimide (NEM) The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da PRIDE:PRIDE The chemical reagent that is used to break disulfide bonds in proteins PRIDE PRIDE:0000607 Reduction reagent The chemical reagent that is used to break disulfide bonds in proteins PRIDE:PRIDE The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2 PRIDE PRIDE:0000608 Dithiothreitol (DTT) The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2 PRIDE:PRIDE The reduction agent with chemincal formuls C9H15O6P PRIDE PRIDE:0000609 Tris(2-carboxyethyl)phosphine (TCEP) The reduction agent with chemincal formuls C9H15O6P PRIDE:PRIDE The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS PRIDE PRIDE:0000610 Beta-mercaptoethanol (BME) The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS PRIDE:PRIDE 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) PRIDE PRIDE:0000612 The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6) SILAC light L:12C(6) 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) PRIDE PRIDE:0000614 The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5) SILAC light P:12C(5) 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) PRIDE PRIDE:0000616 The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6) SILAC heavy L:13C(6) 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) 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) 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) PRIDE PRIDE:0000620 Metabolic label 15N 15N PRIDE PRIDE:0000621 Metabolic label 13C 13C PRIDE PRIDE:0000622 Metabolic label 18O 18O PRIDE PRIDE:0000623 Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics original source name PRIDE PRIDE:0000624 Spectra Cluster Maximum Ratio for the cluster SpectraCluster MaxRatio PRIDE PRIDE:0000625 NIST Probability Correlation NIST ProbCorr PRIDE PRIDE:0000626 NIST best dot product NIST Dotbest PRIDE PRIDE:0000627 Data-dependent acquisition Data-dependent acquisition PRIDE PRIDE:0000629 Parallel Reaction Monitoring (PRM) Parallel reaction monitoring PRIDE PRIDE:0000630 Selected reaction monitoring (SRM) Selected reaction monitoring PRIDE PRIDE:0000631 Mass spectrometry imaging Mass spectrometry imaging TMT133N PRIDE PRIDE:0000632 TMT133N TMT133N PRIDE:PRIDE TMT133C PRIDE PRIDE:0000633 TMT133C TMT133C PRIDE:PRIDE TMT134 PRIDE PRIDE:0000634 TMT134 TMT134 PRIDE:PRIDE 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 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 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 PRIDE PRIDE:0000638 Instrument model Instrument model PRIDE:PRIDE Somalogic instrument model PRIDE PRIDE:0000639 Somalogic instrument model Somalogic instrument model PRIDE:PRIDE SomaScan assay v4.0 PRIDE PRIDE:0000640 SomaScan assay v4.0 SomaScan assay v4.0 PRIDE:PRIDE SomaScan assay v4.1 PRIDE PRIDE:0000641 SomaScan assay v4.1 SomaScan assay v4.1 PRIDE:PRIDE TMT134C PRIDE PRIDE:0000642 TMT134C TMT134C PRIDE:PRIDE TMT134N PRIDE PRIDE:0000643 TMT134N TMT134N PRIDE:PRIDE Fragmentation method used for dissociation or fragmentation for MS2 PRIDE PRIDE:0000644 MS2 dissociation method Fragmentation method used for dissociation or fragmentation for MS2 PRIDE:PRIDE Fragmentation method used for dissociation or fragmentation for MS3 PRIDE PRIDE:0000645 MS3 dissociation method Fragmentation method used for dissociation or fragmentation for MS3 PRIDE:PRIDE MS3 mass analyzer PRIDE PRIDE:0000646 MS3 mass analyzer MS3 mass analyzer PRIDE:PRIDE PRIDE PRIDE:0000649 Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome. Immunopeptidomics Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 PRIDE PRIDE:0000650 diaPASEF Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 PRIDE:PRIDE Absolute quantification precisely measures the concentration of a specific analyte in a sample PRIDE PRIDE:0000651 Absolute quantification Absolute quantification precisely measures the concentration of a specific analyte in a sample PRIDE:PRIDE Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples PRIDE PRIDE:0000652 Relative quantification Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples PRIDE:PRIDE Normalized Protein eXpression PRIDE PRIDE:0000653 NPX Normalized Protein eXpression PRIDE:PRIDE Olink instrument model PRIDE PRIDE:0000654 Olink instrument model Olink instrument model PRIDE:PRIDE Olink Target 96 PRIDE PRIDE:0000655 Olink Target 96 Olink Target 96 PRIDE:PRIDE Olink Explore 1536 PRIDE PRIDE:0000656 Olink Explore 1536 Olink Explore 1536 PRIDE:PRIDE Olink Explore 3072 PRIDE PRIDE:0000657 Olink Explore 3072 Olink Explore 3072 PRIDE:PRIDE Olink Explore 384 PRIDE PRIDE:0000658 Olink Explore 384 Olink Explore 384 PRIDE:PRIDE proteomics data acquisition method PRIDE PRIDE:0000659 Proteomics data acquisition method proteomics data acquisition method PRIDE:PRIDE Ion Mobility Separation PRIDE PRIDE:0000660 Ion Mobility Separation Ion Mobility Separation PRIDE:PRIDE Differential mobility Separation PRIDE PRIDE:0000661 Differential mobility Separation Differential mobility Separation PRIDE:PRIDE SelexION differential mobility separation device PRIDE PRIDE:0000662 SelexION Separation Method SelexION differential mobility separation device PRIDE:PRIDE The technology type or platform used to perform the study. PRIDE PRIDE:0000663 technology type The technology type or platform used to perform the study. EFO:EFO_0005521 An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry PRIDE PRIDE:0000664 proteomic profiling by mass spectrometry An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry EFO:EFO_0002766 Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications. PRIDE PRIDE:0000665 Glycoproteomics Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications. PRIDE:PRIDE TMT 6-plex labeling kit has 6 channels PRIDE PRIDE:0000666 TMT6PLEX TMT 6-plex labeling kit has 6 channels PRIDE:PRIDE TMT 10-plex labeling kit has 10 channels PRIDE PRIDE:0000667 TMT10PLEX TMT 10-plex labeling kit has 10 channels PRIDE:PRIDE TMT 16-plex labeling kit has 16 channels PRIDE PRIDE:0000668 TMT16PLEX TMT 16-plex labeling kit has 16 channels PRIDE:PRIDE TMT 18-plex labeling kit has 18 channels PRIDE PRIDE:0000669 TMT18PLEX TMT 18-plex labeling kit has 18 channels PRIDE:PRIDE TMT135 PRIDE PRIDE:0000670 TMT135 TMT135 PRIDE:PRIDE