Proteomics Standards Initiative
Overview of Project
The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.
The main organizational unit of the Proteomics Standards Initiative is the work group. Currently, there are the following work groups:.
- Molecular Interactions (MI)
- Mass Spectrometry (MS)
- Proteomics Informatics (PI)
- Protein Modifications (MOD)
- Protein Separation (PS)
The standard deliverables of each work group are
- Minimum Information Specification: For the given domain, this specifies the minimum information required for the useful reporting of experimental results in this domain.
- Formal exchange format for experimental results in the domain. This will usually be an XML format, capable of representing at least the Minimum Information, and normally significant additional detail.
- Controlled vocabularies.
- Support for implementation of the standard in publicly available tools.
Collaborations with other Initiatives
The HUPO PSI has a subsidiary role supporting other HUPO projects and workgroups, aiming to ensure collaboration and consistency in the data management approaches taken by the HUPO proteomics initiatives. We continued to data management and long-term data repository support for the HUPO Plasma Proteome (I), Brain and Liver Proteome Projects. Currently, major proteomics repositories represented in the PSI mass spectrometry work group (PRIDE, PeptideAtlas, Tranche) are defining the systematic data capture for the second phase of the Plasma Proteome Project, as well as for the proposed joint HUPO project. A first, large scale dataset for HUPO PPP II has been processed through the proposed pipeline. In the context of the EU ProteomeBinders project, an ongoing collaboration with the HUPO Antibody initiative had significant impact on the recently released “Community standard for the representation of protein affinity reagents (PSI-PAR)”.
A successful interaction with the HUPO publications committee (joint workshops) has resulted in strong connections to key proteomics journals, highly valuable for dissemination and implementation of PSI standards.
Future meetings with dedicated sessions
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TBA
Website Link
Key Documents related to activities
- 2010 Report to the HUPO Council from the PSI
- Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data. Proteomics. 2009 Oct 15;9(22):5112-5119. [Epub ahead of print] PubMed PMID: 19834897.
- Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H. Annual spring meeting of the Proteomics Standards Initiative. Proteomics. 2009 Oct;9(19):4429-32. PubMed PMID: 19670378.
- Orchard S, Binz PA, Hermjakob H. Second Joint HUPO publication and Proteomics Standards Initiative workshop. Proteomics. 2009 Oct;9(19):4426-8. PubMed PMID: 19670377.
- David E. Gloriam, Sandrine Palcy, Sandra Orchard, Luisa Montecchi-Palazzi, Samuel Kerrien, Julie Bourbeillon, Erik Björling, Volker Sievert, Niall Haslam, Peter Woollard, Antoine Daruvar, Oda Stoevesandt, Michael J. Taussig, David J. Sherman and Henning Hermjakob. Report: A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics. 2009 Aug 13. [Epub ahead of print] PubMed PMID: 19674966.
- Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H. Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. Proteomics. 2008 Oct;8(20):4168-72. PubMed PMID: 18814335.
- Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz PA, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol. 2008 Aug;26(8):863-4. PubMed PMID: 18688234.
- Binz PA, Barkovich R, Beavis RC, Creasy D, Horn DM, Julian RK Jr, Seymour SL, Taylor CF, Vandenbrouck Y. Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol. 2008 Aug;26(8):862. PubMed PMID: 18688233.
- Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK Jr. Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol. 2008 Aug;26(8):860-1. PubMed PMID: 18688232.
- Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS. The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol. 2008 Aug;26(8):864-6. PubMed PMID: 18688235.
- Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 9;5:44.
- Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.: The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug;25(8):894-8. PMID: 17687370
- Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.: The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007 Aug;25(8):887-93. PMID: 17687369
- Vizcaino JA, Martens L, Hermjakob H, Julian RK, Paton NW. The PSI formal document process and its implementation on the PSI website. Proteomics. 2007 Jul;7(14):2355-7. PMID: 17570517
