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 contribute 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.
Website Link
Key Documents related to activities
Publications 2010-2011
- Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci. 2010 Dec 25;3(3):259-66. PubMed PMID: 21304730; PubMed Central PMCID: PMC3035314.
- Orchard S, Jones A, Albar JP, Cho SY, Kwon KH, Lee C, Hermjakob H. Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics. 2010 Sep;10(17):3062-6. PubMed PMID: 20806224.
- Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW. mzML--a community standard for mass spectrometry data. Mol Cell Proteomics. 2011 Jan;10(1):R110.000133. Epub 2010 Aug 17. PubMed PMID: 20716697; PubMed Central PMCID: PMC3013463.
- Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics. 2010 Sep;10(17):3073-81. PubMed PMID: 20677327; PubMed Central PMCID: PMC3193076.
- Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H. implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics. 2010 May;10(10):1895-8. PubMed PMID: 20623474.
- Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PA, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D. Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol. 2010 Jul;28(7):650-3. PubMed PMID: 20622827.
- Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics. 2010 Jan;9(1):1-10. Epub 2009 Aug 11. PubMed PMID: 19674966; PubMed Central PMCID: PMC2808255.
- Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. 2012 Jan;12(1):11-20. doi: 10.1002/pmic.201100562. Epub 2011 Dec 14. PubMed PMID: 22069307.
- Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H. Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics. 2011 Nov;11(22):4284-90. doi: 10.1002/pmic.201190117. PubMed PMID: 22045680.
- Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov. 2011 Aug 31;10(9):661-9. doi: 10.1038/nrd3503. Review. PubMed PMID: 21878981.
- Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. PubMed PMID: 21716279; PubMed Central PMCID: PMC3246345.
- Orchard S, Hermjakob H. Data standardization by the HUPO-PSI: how has the community benefitted? Methods Mol Biol. 2011;696:149-60. PubMed PMID: 21063946.
Earlier Documents - Publications
