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.

Taxonomic range

Scope and data types

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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	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Gel electrophoresis Markup Language	PSI GelML	Standard	Assay Electrophoresis Extract Life Science Material component separation Plus 3 more...	All	PRIDE	sepCV PSI-MS CV mzML PSI SpML HUPO-PSI TraML Plus 3 more...	None	FAIRDOM Community Standards HUPO Proteomics Standards Initiative
HUPO PSI Mass Spectrometry Controlled Vocabulary	PSI-MS CV	Standard	Life Science Mass spectrometry assay Protein Proteomics	All	MTBLS GMD jPOSTrepo OBO	mzQuantML mzIdentML PSI GelML	None	OBO Foundry H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack FAIRDOM Community Standards HUPO Proteomics Standards Initiative
MIAPE: Capillary Electrophoresis	MIAPE-CE	Standard	Assay Electrophoresis Life Science Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIMIx MIAPE MIAPE-Quant MIAPE-MS MIAPE-GE Plus 4 more...	None	HUPO Proteomics Standards Initiative
MIAPE: Column Chromatography	MIAPE-CC	Standard	Assay Chromatography Life Science Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIMIx MIAPE MIAPE-Quant MIAPE-MS MIAPE-GE Plus 4 more...	None	HUPO Proteomics Standards Initiative
MIAPE: Gel Electrophoresis	MIAPE-GE	Standard	Assay Electrophoresis Life Science Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIMIx MIAPE MIAPE-Quant MIAPE-MS MIAPE-GI Plus 5 more...	GTL Program Information and Data Sharing Policy	HUPO Proteomics Standards Initiative
MIAPE: Gel Informatics	MIAPE-GI	Standard	Assay Life Science Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteoRed	MIMIx MIAPE MIAPE-Quant MIAPE-MS MIAPE-GE Plus 4 more...	None	HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry	MIAPE-MS	Standard	Assay Life Science Mass spectrometry spectra Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteomeXchange ProteoRed jPOSTrepo	mzML MIMIx MIAPE MIAPE-Quant MIAPE-GE Plus 5 more...	GTL Program Information and Data Sharing Policy	HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry Informatics	MIAPE-MSI	Standard	Assay Life Science Mass spectrometry spectra Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE ProteomeXchange ProteoRed	mzML imzML MIMIx MIAPE MIAPE-Quant Plus 6 more...	GTL Program Information and Data Sharing Policy	HUPO Proteomics Standards Initiative
MIAPE: Mass Spectrometry Quantification	MIAPE-Quant	Standard	Assay Life Science Mass spectrometry spectra Protein Proteomics Plus 1 more...	Archaea Bacteria Eukaryota	ProteoRed	mzQuantML MIMIx MIAPE MIAPE-MS MIAPE-GE Plus 5 more...	None	HUPO Proteomics Standards Initiative
Minimum Information About a Bioactive Entity	MIABE	Standard	Bioactivity Biomarker Biomedical Science Drug Target Life Science Plus 3 more...	All	canSAR	LINCS 2: Small molecules MIAPE MIMIx PSI-MI CV	None	Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative
Minimum Information about a Molecular Interaction Experiment	MIMIx	Standard	Assay Biochemistry Chemical entity Deoxyribonucleic acid (DNA) Interactome Plus 5 more...	Archaea Bacteria Eukaryota	IntAct MINT MatrixDB ProteoRed	PSI-MI XML PSI-MI CV MITAB MIAPAR MIAPE Plus 8 more...	EMBO Recommended Databases and Data Standards Springer Nature - Research Data Policies Springer Nature Research Data Policy Type 1 Springer Nature Research Data Policy Type 4 Rockefeller University Press - Journal Of Cell Biology - Data Deposition Plus 6 more...	FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative Chemistry
Minimum Information about a Protein Affinity Reagent	MIAPAR	Standard	Assay Intensity Life Science Protein Reagent	All	None	PSI-PAR XML MIMIx MIAPE PSI-MI CV PSI-PAR CV	None	Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative
Minimum Information About a Proteomics Experiment	MIAPE	Standard	Assay Life Science Pathogen Protein Proteomics	Archaea Bacteria Eukaryota	PRIDE World-2DPAGE ProteomeXchange ProteoRed	sepCV ISA-Tab PSI-MI XML mzML 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 Minimum Information for Biological and Biomedical Investigations HUPO Proteomics Standards Initiative
Minimum Information About Sample Preparation for a Phosphoproteomics Experiment	MIASPPE	Standard	Amino acid sequence Assay Chromatography Life Science Mass spectrometry spectra Plus 5 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 Molecular interaction Protein Proteomics	All	IntAct MINT Gene3D TopFIND InteroPorc Plus 9 more...	PSI-PAR XML XML MIMIx MIAPE MITAB Plus 1 more...	None	International Molecular Exchange Consortium (IMEx) HUPO Proteomics Standards Initiative
Molecular Interaction Tabular	MITAB	Standard	Life Science Molecular interaction Protein Proteomics	All	IntAct MINT PINA TopFIND InteroPorc Plus 13 more...	MIMIx PSI-MI XML PSI-MOD PSI-MI CV	None	International Molecular Exchange Consortium (IMEx) HUPO Proteomics Standards Initiative
~~mzData~~	~~mzData~~	Standard	Life Science Mass spectrometry spectra Proteomics	Not applicable	None	mzML	None	Metabolomics Standards and Databases HUPO Proteomics Standards Initiative
mz Markup Language	mzML	Standard	Centrally registered identifier Life Science Mass spectrometry assay Mass spectrometry spectra Protein	All	MOPED MitoZoa PRIDE PeptideAtlas World-2DPAGE Plus 2 more...	mzQuantML imzML PSI SpML MIAPE mzData Plus 7 more...	EMBO Recommended Databases and Data Standards	Metabolomics Standards and Databases H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project eTRIKS Standards Starter Pack FAIRDOM Community Standards HUPO Proteomics Standards Initiative
mz peptide and protein Identification Markup Language	mzIdentML	Standard	Centrally registered identifier Life Science Peptide identification Protein Protein identification	All	MassIVE	mzQuantML PSI-MS CV PSI SpML QCML mzTab Plus 1 more...	None	HUPO Proteomics Standards Initiative
mz Quantitative Markup Language	mzQuantML	Standard	Experimental measurement Life Science Protein Quantification	All	PRIDE	PSI-MS CV mzIdentML mzML PSI SpML HUPO-PSI TraML Plus 4 more...	None	HUPO Proteomics Standards Initiative
mzTab	mzTab	Standard	Data sharing Life Science Proteomics	All	jPOSTrepo MassIVE	mzQuantML mzIdentML	None	HUPO Proteomics Standards Initiative
proBed	proBed	Standard	Life Science Peak matching Peptide-spectrum matching Protein sequence Proteogenomics	All	Ensembl	BED	None	HUPO Proteomics Standards Initiative
Protein Affinity Reagent Controlled Vocabulary	PSI-PAR CV	Standard	Affinity Life Science Molecular interaction Protein	All	None	MIAPAR PSI-PAR XML PSI-MI XML	None	HUPO Proteomics Standards Initiative
Protein MODification	PSI-MOD	Standard	Enzymatic reaction Life Science Protein	All	MnM PomBase TopFIND OBO CP	ProForma MITAB	None	OBO Foundry FAIRDOM Community Standards HUPO Proteomics Standards Initiative
PSI Molecular Interaction Controlled Vocabulary	PSI-MI CV	Standard	Life Science Molecular interaction Protein Protein interactions	All	ELM MINT modMine PINA APID Interactomes Plus 4 more...	MITAB MIAPAR MIMIx INO ReTO Plus 3 more...	Elsevier Data Policy	OBO Foundry HUPO Proteomics Standards Initiative
Quality Control Markup Language	QCML	Standard	Chromatin immunoprecipitation - DNA sequencing (ChIP-seq) Life Science Metabolomics Proteomics Quality control Plus 1 more...	All	None	mzQuantML mzIdentML mzML XML	None	HUPO Proteomics Standards Initiative
Sample processing and separations controlled vocabulary	sepCV	Standard	Life Science Material processing Protein Proteomics Sample preparation for assay	All	OBO	PSI GelML PSI SpML MIAPE	None	OBO Foundry HUPO Proteomics Standards Initiative
Separation Markup Language	PSI SpML	Standard	Life Science Material component separation Protein	All	None	mzIdentML mzQuantML PSI GelML sepCV imzML Plus 2 more...	None	HUPO Proteomics Standards Initiative
Transition Markup Language	HUPO-PSI TraML	Standard	Life Science Mass spectrometry assay Proteomics	All	PRIDE	mzQuantML PSI GelML XML	None	HUPO Proteomics Standards Initiative

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