Abstract
Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling 'MIAPE-compliant' reporting.
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References
Cochrane, G., et al. EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res. 34 (Database issue) D10–D15 (2006).
Galperin, M.Y. The molecular biology database collection: 2006 update. Nucleic Acids Res. 34 (Database issue), D3–D5 (2006).
Ball, C.A., et al. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 33 (Database issue), D580–D582 (2005).
Brazma, A. et al. ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68–71 (2003).
Barrett, T. & Edgar, R. Gene Expression Omnibus (GEO): microarray data storage, submission, retrieval, and analysis. Methods Enzymol. 411, 352–369 (2006).
Wu, C.H., et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34 (Database issue) D187–D191 (2006).
Birney, E., et al. Ensembl 2006. Nucleic Acids Res. 34 (Database issue), D556–D561 (2006).
Pruitt, K.D., Tatusova, T., Maglott, D.R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33 (Database issue) D501–D504 (2005).
Appel, R.D. et al. Federated 2-DE database: a simple means of publishing 2-DE data. Electrophoresis 17, 540–546 (1996).
Babnigg, G., Giometti, C.S. GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. Nucleic Acids Res. 32 (Database issue), D582–D585 (2004).
Garwood, K. et al. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics [online] 5, 68 (2004).
Jones, P., et al. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34 (Database issue), D659–D663 (2006).
Prince, J.T. et al. The need for a public proteomics repository. Nat. Biotechnol. 22, 471–472 (2004).
Craig, R., Cortens, J.P. & Beavis, R.C. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3, 1234–1242 (2004).
Hogan, J.M., Higdon, R. & Kolker, E. Experimental standards for high throughput proteomics. OMICS 10, 152–157 (2006).
Lenth, R.V. Some practical guidelines for effective sample size determination. Am. Stat. 55, 187–193 (2001).
Orchard, S., Hermjakob, H. & Apweiler, R. The proteomics standards initiative. Proteomics 3, 1374–1376 (2003).
Hermjakob, H. The HUPO Proteomics Standards Initiative — overcoming the fragmentation of proteomics data. Proteomics 6 (suppl. 2), 34–38 (2006).
Brazma, A. et al. Minimum information about a microarray experiment (MIAME) — toward standards for microarray data. Nat. Genet. 29, 365–371 (2001).
Anonymous. Microarray standards at last. Nature 419, 323 (2002).
Ball, C.A. et al. A guide to microarray experiments—an open letter to the scientific journals. Lancet 360, 1019 (2002).
Information for authors. Cell Online <http://www.cell.com/misc/page?page=authors> (2006).
Sreenu, V.B., Kumar, P., Nagaraju, J. & Nagarajaram, H.A. Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity. BMC Genomics [online] 7, 78 (2006).
Albers, C.J., Jansen, R.C., Kok, J., Kuipers, O.P. & van Hijum, S.A. SIMAGE: simulation of DNA-microarray gene expression data. BMC Bioinformatics [online] 7, 205 (2006).
Larsson, O. & Sandberg, R. Lack of correct data format and comparability limits future integrative microarray research. Nat. Biotechnol. 24, 1322–1323 (2006).
Burgoon, L.D. The need for standards, not guidelines, in biological data reporting and sharing. Nat. Biotechnol. 24, 1369–1373 (2006).
Edgar, R. & Barrett, T. NCBI GEO standards and services for microarray data. Nat. Biotechnol. 24, 1471–1472 (2006).
Moher, D., Schulz, K.F. & Altman, D.G. The CONSORT statement: revised recommendations for improving the quality of reports of parallel-group randomised trials. Lancet 357, 1191–1194 (2001).
Moher, D. et al. Improving the quality of reports of meta-analyses of randomised controlled trials: the QUOROM statement. Lancet 354, 1896–1900 (1999).
Bossuyt, P.M. et al. Towards complete and, accurate reporting of studies of diagnostic accuracy: the STARD initiative. Br. Med. J. 326, 41–44 (2003).
McShane, L.M. et al. REporting recommendations for tumour MARKer prognostic studies (REMARK). Eur. J. Cancer 41, 1690–1696 (2005).
CDISC SEND Team. Standard for exchange of nonclinical data (SEND). Implementation guide for animal toxicology studies. Version 2.3. CDISC Standards <http://www.cdisc.org/models/send/v2.3> (2005).
Plint, A.C. et al. Does the CONSORT checklist improve the quality of reports of randomised controlled trials? A systematic review. Med. J. Aust. 185, 263–267 (2006).
Smidt, N. et al. The quality of diagnostic accuracy studies since the STARD statement—has it improved? Neurology 67, 792–797 (2006).
Taylor, C.F. et al. Promoting coherent minimum reporting requirements for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol. (in the press).
Wilkins, M.R., Williams, K.L., Appel, R.D. & Hochstrasser, D.F. (eds.) Proteome Research: New Frontiers in Functional Genomics (Springer, Berlin, 1997).
Pennington, S.R. & Dunn, M.J. (eds.) Proteomics: From Protein Sequence to Function. (BIOS, Oxford, 2001).
BBSRC's data sharing policy. BBSRC: Biotechnology and Biological Sciences Research Council <http://www.bbsrc.ac.uk/support/guidelines/datasharing/context.html> (2006).
Publication guidelines for the analysis and documentation of peptide and protein identifications. Molecular & Cellular Proteomics <http://www.mcponline.org/misc/ParisReport_Final.shtml> (2007).
Carr, S. et al. The need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and protein identification data. Mol. Cell. Proteomics 3, 531–533 (2004).
Wilkins, M.R. et al. Guidelines for the next 10 years of proteomics. Proteomics 6, 4–8 (2006).
Rauch, A. et al. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 5, 112–121 (2006).
Brazma, A. & Parkinson, H. ArrayExpress service for reviewers/editors of DNA microarray papers. Nat. Biotechnol. 24, 1321–1322 (2006).
Noble, W.S. Data hoarding is harming proteomics. Nat. Biotechnol. 22, 1209 (2004).
Quackenbush, J. Standardizing the standards. Mol. Syst. Biol. 2, 2006.0010 (2006).
Orchard, S. et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 25, 894–898 (2007).
Acknowledgements
The people who have contributed to the evolution of this document are too numerous to name, but it is important to note the contribution made by the PSI's many participants, who have contributed through attendance at meetings, web-based discussion and other forms of communication. Many others have also commented, at conferences and elsewhere: academics, commercial scientists, vendors, funders, editors and others.
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Taylor, C., Paton, N., Lilley, K. et al. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25, 887–893 (2007). https://doi.org/10.1038/nbt1329
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DOI: https://doi.org/10.1038/nbt1329
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