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HUPO Proteomics Standards Initiative

The HUPO Proteomics Standards Initiative (HUPO PSI) defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. It was founded at the HUPO meeting in Washington, April 28-29, 2002.

This record is maintained by: HUPOPSI

Record added: Feb. 28, 2017, 11:41 a.m..
Record updated: Sept. 2, 2017, 3:12 p.m. by HUPOPSI.

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Edits to 'https://fairsharing.org/bsg-c000038' by 'The FAIRsharing Team' at 11:44, 28 Feb 2017 (approved):

	'description' has been modified:
		Before: The HUPO Proteomics Standards Initiative (HUPO PSI) defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. It was founded at the HUPO meeting in Washington, April 28-29, 2002.
		After: The HUPO Proteomics Standards Initiative (HUPO PSI) defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. It was founded at the HUPO meeting in Washington, April 28-29, 2002.

Edits to 'https://fairsharing.org/bsg-c000038' by 'HUPOPSI' at 15:12, 02 Sep 2017 (approved):

	'standards' has been modified:
		Before:
			mz peptide and protein Identification Markup Language
			mz Quantitative Markup Language
			Sample processing and separations controlled vocabulary
			HUPO PSI Mass Spectrometry Controlled Vocabulary
			Protein Affinity Reagent Controlled Vocabulary
			PSI Molecular Interaction Controlled Vocabulary
			Transition Markup Language
			Protein MODification
			Molecular Interaction eXtensible Markup Language
			mz Markup Language
			Molecular Interaction Tabular
			Separation Markup Language
			Minimum Information About a Proteomics Experiment
			Minimum Information about a Protein Affinity Reagent
			Minimum Information About Sample Preparation for a Phosphoproteomics Experiment
			Minimum Information about a Molecular Interaction Experiment
			MIAPE: Mass Spectrometry Quantification
			MIAPE: Gel Informatics
			MIAPE: Mass Spectrometry
			MIAPE: Mass Spectrometry Informatics
			MIAPE: Gel Electrophoresis
			mzData
			MIAPE: Capillary Electrophoresis
			MIAPE: Column Chromatography
			Gel electrophoresis Markup Language
			proBed
			mzTab
			Minimum Information About a Bioactive Entity
		After:
			mz peptide and protein Identification Markup Language
			mz Quantitative Markup Language
			Sample processing and separations controlled vocabulary
			HUPO PSI Mass Spectrometry Controlled Vocabulary
			Protein Affinity Reagent Controlled Vocabulary
			PSI Molecular Interaction Controlled Vocabulary
			Transition Markup Language
			Protein MODification
			Molecular Interaction eXtensible Markup Language
			mz Markup Language
			Molecular Interaction Tabular
			Separation Markup Language
			Minimum Information About a Proteomics Experiment
			Minimum Information about a Protein Affinity Reagent
			Minimum Information About Sample Preparation for a Phosphoproteomics Experiment
			Minimum Information about a Molecular Interaction Experiment
			MIAPE: Mass Spectrometry Quantification
			MIAPE: Gel Informatics
			MIAPE: Mass Spectrometry
			MIAPE: Mass Spectrometry Informatics
			MIAPE: Gel Electrophoresis
			mzData
			MIAPE: Capillary Electrophoresis
			MIAPE: Column Chromatography
			Gel electrophoresis Markup Language
			proBed
			mzTab
			Minimum Information About a Bioactive Entity
			Quality Control Markup Language
		Added:
			Quality Control Markup Language
		Removed:

Publications

Proteomics. Public-private group maps out initiatives.

Kaiser J
Science 2002

View Paper (PubMed) View Publication

The Proteomics Standards Initiative

Sandra Orchard, Henning Hermjakob, Rolf Apweiler
Proteomics 2003

View Paper (PubMed) View Publication

29 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Gel electrophoresis Markup Language	PSI GelML	Standard	Life Science Proteomics	Report Assay Electrophoresis Extract Material component separation Plus 2 more...	All	PRIDE	PSI-MS CV sepCV mzML PSI SpML PRIDE XML Format Plus 3 more...	None	FAIRDOM Community Standards HUPO Proteomics Standards Initiative ISO/CD 20691 Collection - DRAFT
HUPO PSI Mass Spectrometry Controlled Vocabulary	PSI-MS CV	Standard	Life Science Proteomics	Mass spectrometry assay Protein	All	MTBLS GMD jPOSTrepo OBO	mzQuantML mzIdentML UO PSI GelML PRIDE XML Format Plus 1 more...	None	H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards eTRIKS Standards Starter Pack HUPO Proteomics Standards Initiative
MIAPE: Capillary Electrophoresis	MIAPE-CE	Standard	Life Science Proteomics	Assay Electrophoresis Protein	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIAPE-Quant MIAPE-MSI MIAPE-CC MIAPepAE MIAPE-GE Plus 4 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Column Chromatography	MIAPE-CC	Standard	Life Science Proteomics	Assay Chromatography Protein	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIAPE-Quant MIAPE-CE MIAPE-GE MIAPE-GI MIAPepAE Plus 4 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Gel Electrophoresis	MIAPE-GE	Standard	Life Science Proteomics	Assay Electrophoresis	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIMIx MIAPE MIAPE-Quant MIAPE-MSI MIAPE-GI Plus 5 more...	GTL Program Information and Data Sharing Policy	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Gel Informatics	MIAPE-GI	Standard	Life Science Proteomics	Assay Protein	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIAPE-CE MIAPE-Quant MIAPE-GE MIAPE-CC MIAPepAE Plus 4 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry	MIAPE-MS	Standard	Life Science Proteomics	Mass spectrometry spectra Assay Protein	Archaea Bacteria Eukaryota	PRIDE ProteomeXchange ProteoRed jPOSTrepo	mzML MIMIx MIAPE MIAPE-Quant MIAPE-MSI Plus 5 more...	GTL Program Information and Data Sharing Policy	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry Informatics	MIAPE-MSI	Standard	Life Science Proteomics	Mass spectrometry spectra Assay Protein	Archaea Bacteria Eukaryota	PRIDE ProteomeXchange ProteoRed	mzML imzML MIMIx MIAPE MIAPE-Quant Plus 6 more...	GTL Program Information and Data Sharing Policy	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry Quantification	MIAPE-Quant	Standard	Life Science Proteomics	Mass spectrometry spectra Quantification Assay Protein	Archaea Bacteria Eukaryota	ProteoRed	mzQuantML MIMIx MIAPE MIAPE-MSI MIAPE-GI Plus 5 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
Minimum Information About a Bioactive Entity	MIABE	Standard	Biomedical Science Toxicology	Bioactivity Biomarker Molecular entity Molecular interaction Small molecule Plus 2 more...	All	canSAR	PSI-MI CV LINCS 2: Small molecules MIMIx MIAPE	None	HUPO Proteomics Standards Initiative Minimum Information for Biological and Biomedical Investigations ISO/CD 20691 Collection - DRAFT
Minimum Information about a Molecular Interaction Experiment	MIMIx	Standard	Biochemistry Life Science Proteomics	Assay Chemical entity Deoxyribonucleic acid Interactome Lipid Plus 2 more...	Archaea Bacteria Eukaryota	IntAct MINT MatrixDB DIP ProteoRed	PSI-MI CV MITAB PSI-MI XML MIAPAR MIAPE Plus 9 more...	Springer Nature Research Data Policy Type 1 Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 4 EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Plus 6 more...	FAIRDOM Community Standards HUPO Proteomics Standards Initiative Minimum Information for Biological and Biomedical Investigations Chemistry
Minimum Information about a Protein Affinity Reagent	MIAPAR	Standard	Life Science	Assay Intensity Protein Reagent	All	None	PSI-PAR XML PSI-MI CV PSI-PAR CV MIMIx MIAPE	None	HUPO Proteomics Standards Initiative Minimum Information for Biological and Biomedical Investigations ISO/CD 20691 Collection - DRAFT
Minimum Information About a Proteomics Experiment	MIAPE	Standard	Life Science Proteomics	Experimental measurement Assay Experimentally determined Pathogen Protein Plus 2 more...	Archaea Bacteria Eukaryota	PRIDE gpmDB World-2DPAGE ProteomeXchange ProteoRed	ISA-Tab sepCV mzML PSI-MI XML imzML Plus 13 more...	EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition SciData Data Policy Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition	FAIRDOM Community Standards HUPO Proteomics Standards Initiative Minimum Information for Biological and Biomedical Investigations ISO/CD 20691 Collection - DRAFT
Minimum Information About Sample Preparation for a Phosphoproteomics Experiment	MIASPPE	Standard	Life Science Proteomics	Mass spectrometry spectra Assay Chromatography Peptide Phosphoprotein Plus 3 more...	All	ENA	MIAPE	None	Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative
Molecular Interaction eXtensible Markup Language	PSI-MI XML	Standard	Life Science Proteomics	Molecular interaction Protein	All	IntAct MINT Gene3D TopFIND InteroPorc Plus 10 more...	MITAB XML PSI-PAR XML PSI-PAR CV MIMIx Plus 1 more...	EMBO Recommended Databases and Data Standards	International Molecular Exchange Consortium (IMEx) HUPO Proteomics Standards Initiative ISO/CD 20691 Collection - DRAFT
Molecular Interaction Tabular	MITAB	Standard	Life Science Proteomics	Molecular interaction Protein	All	IntAct MINT PINA TopFIND InteroPorc Plus 14 more...	PSI-MI CV PSI-MOD PSI-MI XML MIMIx	EMBO Recommended Databases and Data Standards	HUPO Proteomics Standards Initiative International Molecular Exchange Consortium (IMEx)
~~mzData~~	~~mzData~~	Standard	Life Science Proteomics	Mass spectrometry spectra	Not applicable	None	mzML	None	ISO/CD 20691 Collection - DRAFT Metabolomics Standards and Databases HUPO Proteomics Standards Initiative
mz Markup Language	mzML	Standard	Life Science	Mass spectrometry spectra Centrally registered identifier Mass spectrometry assay Protein	All	MOPED MitoZoa PRIDE PeptideAtlas World-2DPAGE Plus 2 more...	mzQuantML PSI SpML imzML MIAPE mz5 Plus 7 more...	EMBO Recommended Databases and Data Standards Advanced Genetics	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards eTRIKS Standards Starter Pack HUPO Proteomics Standards Initiative Plus 2 more...
mz peptide and protein Identification Markup Language	mzIdentML	Standard	Life Science	Peptide identification Protein identification Centrally registered identifier Protein	All	MassIVE	PSI-MS CV mzQuantML PSI SpML QCML mzTab Plus 1 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
mz Quantitative Markup Language	mzQuantML	Standard	Life Science	Experimental measurement Quantification Protein	All	PRIDE	PSI-MS CV MIAPE-Quant mzTab QCML mzIdentML Plus 4 more...	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
mzTab	mzTab	Standard	Life Science Proteomics	None	All	jPOSTrepo MassIVE	mzTab-M mzQuantML mzIdentML	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
proBed	proBed	Standard	Life Science Proteogenomics	Mass spectrometry spectra Peak matching polypeptide_region Protein Protein modification Plus 1 more...	All	Ensembl	BED proBAM	None	RDA Covid-19 WG Resources ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
Protein Affinity Reagent Controlled Vocabulary	PSI-PAR CV	Standard	Life Science	Affinity Molecular interaction Protein	All	None	MIAPAR PSI-PAR XML PSI-MI XML	None	HUPO Proteomics Standards Initiative
Protein MODification	PSI-MOD	Standard	Life Science	Enzymatic reaction Protein	All	MnM PomBase TopFIND Alliance of Genome Resources OBO Plus 1 more...	MI2CAST MITAB ProForma DRAO PRIDE XML Format	None	FAIRDOM Community Standards HUPO Proteomics Standards Initiative
PSI Molecular Interaction Controlled Vocabulary	PSI-MI CV	Standard	Life Science	Protein interaction Molecular interaction Protein	All	ELM MINT modMine PINA APID Interactomes Plus 7 more...	MITAB MIAPAR MIMIx INO ReTO Plus 6 more...	Advanced Genetics	HUPO Proteomics Standards Initiative ISO/CD 20691 Collection - DRAFT Advanced Genetics
Quality Control Markup Language	QCML	Standard	Life Science Metabolomics Proteomics	Chromatin immunoprecipitation - DNA sequencing RNA sequencing Quality control	All	None	mzQuantML mzIdentML mzML XML	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
Sample processing and separations controlled vocabulary	sepCV	Standard	Life Science Proteomics	Material processing Protein Sample preparation for assay	All	OBO	PSI SpML PSI GelML MIAPE	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative
Separation Markup Language	PSI SpML	Standard	Life Science	Material component separation Protein	All	None	mzIdentML mzQuantML sepCV imzML PSI GelML Plus 2 more...	None	HUPO Proteomics Standards Initiative
Transition Markup Language	HUPO-PSI TraML	Standard	Life Science Proteomics	Mass spectrometry assay	All	PRIDE	mzQuantML PSI GelML XML	None	ISO/CD 20691 Collection - DRAFT HUPO Proteomics Standards Initiative

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