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HUPO
Proteomics Standards Initiative

Mission Statement

The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification. The PSI was founded at the HUPO meeting in Washington, April 28-29, 2002 (see Science 296, 827).

News and future events
Project status table
Work groups

Molecular Interactions (MI)
Mass Spectrometry (MS)
Sample Processing (SP)
Gel electrophoresis (Gel)
Proteomics Informatics (PI)
Protein Modifications (Mod)

The Document Store
Publications
Previous events
Mailing lists

News and future events

The PSI Fall Meeting '06, Washington, DC
- Original meeting announcement and agenda
- Meeting minutes to go here soon...
PSI Spring Meeting '06, San Francisco
- Original meeting announcement and agenda
- Meeting minutes

Project status table

*Working Group*	*Reporting Guidelines (MIAPE)*		*Data exchange format*		*Controlled vocabulary*
Cross-WG projects	MIAPE Principles Document	4	FuGE (milestone 3)	4	FuGO	1
	Study design and sample generation	1
	Statistical analysis of data	0
Gel	Gel electrophoresis	4	GelML (milestone 1)	3	Gel CV	2
Gel	Gel image informatics	2	GelInfoML	2	Gel CV	2
Sample Processing	Chromatography	3	spML (milestone 1)	3	SP CV	1
	Capillary electrophoresis	3
	Sample Processing	0
Mass Spectrometry	Mass spectrometry	4	mzData (v1.05)	4	MS CV	3
Mass Spectrometry	Mass spectrometry informatics	4	analysisXML	2	MS CV	3
Molecular Interactions	Molecular interactions	5	MIF	5	PSI-MI (v2.5)	5

Color key:

(0) Nothing

(1) Drafting

(2) Alpha

(3) Beta

(4) Release

(5) Published

Work groups

Molecular Interactions

Several well-established public databases for protein-protein interaction data exist, including BIND, DIP, IntAct, MINT and MIPS. However, the data were originally provided in many different, incompatible formats.

The PSI Molecular Interaction work group develops and maintains a common data standard that allows users to retrieve all relevant data from different sites and perform comparative analysis of different data sets in a consistent format. The standard comprises an XML format and detailed controlled vocabularies, and allows a detailed representation of a fully curated interaction record.

For a detailed documentation of the PSI Molecular Interaction standard, please see http://psidev.sourceforge.net/mi/rel25/ and the Nature Biotechnology paper.

Mass Spectrometry

Widely accepted public repositories for mass spectrometry based protein identifications do not exist at present and detailed experimental results are usually not available.

The PSI Mass Spectrometry work group develops a standard representation of experimental spectra in the context of the experimental setup and the analysed system. Such a format will support publications with detailed experimental results, and will allow data exchange and the comparision of related proteomics experiments beyond the local research team.

PSI-MS Format page.

Sample Processing

The remit of this working group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be 'classical' one- or two-dimensional gel electrophoresis (cf. the Gel WG below), along with other kinds of sample handling and processing (for example, 'tagging' proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics.

Deliverables:

MIAPE CC — reporting requirements for column chromatography

MIAPE CE — reporting requirements for capillary electrophoresis

MIAPE SP — reporting requirements for sample preparation and handling

spML — data format for non-gel-based separations, sample preparation and handling

spCV — supporting controlled vocabulary for spML

Sample Processing Homepage

Gel-based methods of analysis (GEL)

Deliverables:

MIAPE GE — reporting requirements for gel electrophoresis

GelML — data format for gel electrophoresis experiments prior to image analysis

MIAPE GI — reporting requirements for gel informatics

GelInfoML — data format for gel informatics

Gel CV — supporting controlled vocabulary for GelML and GelInfoML

GEL Group Charter (draft)

The PSI-GEL work group is a collaboration of researchers from academia, industrial partners and software vendors. The group aims to develop reporting requirements that supplement the MIAPE parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images.

PSI-GEL page

Proteomics Informatics

Main Deliverable: analysisXML and associated documentation / tools

The PSI Proteomics Informatics standards group is a recent addition to the working groups of the Proteomics Standards Initiative. Please look at the Proteomics Informatics Homepage for more details the activities of the group, including how to get involved.

Proteomics Informatics Group Charter

The PSI Proteomics Informatics (PSI-PI) standards group consists of academic, government and industry researchers, software developers, publishers and instrument manufacturers. The goals of the group are:

to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products.

Publications

Orchard, S., L. Montecchi-Palazzi, et al. (2005). "The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments." Pac Symp Biocomput: 186-96.
Orchard, S., H. Hermjakob, et al. (2005). "Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004." Proteomics 5(2): 337-9.
Orchard, S., H. Hermjakob, et al. (2005). "Second Proteomics Standards Initiative Spring Workshop; Siena, Italy 17-20th April 2005." Exp Review of Proteomics 2(3): 287-289.
Hermjakob, H., L. Montecchi-Palazzi, et al. (2004). "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data." Nat Biotechnol 22(2): 177-83.
Orchard, S., H. Hermjakob, et al. (2004). "Proteomics and Data Standardisation." Drug Discovery Today: BIOSILICO 2(3): 91-93.
Orchard, S., H. Hermjakob, et al. (2004). "Common interchange standards for proteomics data: Public availability of tools and schema." Proteomics 4(2): 490-1.
Orchard, S., C. F. Taylor, et al. (2004). "Advances in the development of common interchange standards for proteomic data." Proteomics 4(8): 2363-5.
Orchard, S., W. Zhu, et al. (2003). "Further advances in the development of a data interchange standard for proteomics data." Proteomics 3(10): 2065-6.
Orchard, S., H. Hermjakob, et al. (2003). "The proteomics standards initiative." Proteomics 3(7): 1374-6.
Orchard, S., P. Kersey, et al. (2003). "The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data." Comparative and Functional Genomics 4: 16-19.
Orchard, S., P. Kersey, et al. (2003). "Progress in establishing common standards for exchanging proteomics data. The second meeting of the HUPO Proteomics Standards Initiative." Comparative and Functional Genomics 4(2): 203-206.