Perspective abstract


Nature Biotechnology 25, 887 - 893 (2007)
Published online: 8 August 2007 | doi:10.1038/nbt1329

The minimum information about a proteomics experiment (MIAPE)

Chris F Taylor1,2, Norman W Paton1,3, Kathryn S Lilley1,4, Pierre-Alain Binz1,5,6, Randall K Julian, Jr1,7, Andrew R Jones1,3, Weimin Zhu1,2, Rolf Apweiler1,2, Ruedi Aebersold1,8, Eric W Deutsch1,9, Michael J Dunn10, Albert J R Heck11, Alexander Leitner12, Marcus Macht13, Matthias Mann14, Lennart Martens1,2, Thomas A Neubert15, Scott D Patterson16, Peipei Ping17, Sean L Seymour1,18, Puneet Souda19, Akira Tsugita20, Joel Vandekerckhove21, Thomas M Vondriska22, Julian P Whitelegge19, Marc R Wilkins23, Ioannnis Xenarios24, John R Yates, III25 & Henning Hermjakob1,2


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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  1. The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  2. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  3. School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
  4. Cambridge Centre for Proteomics, University of Cambridge, Cambridge, Cambridgeshire CB2 1QW, UK.
  5. Swiss Institute of Bioinformatics, Geneva, Switzerland.
  6. GeneBio SA, Geneva, Switzerland.
  7. Indigo BioSystems, Indianapolis, Indiana, USA.
  8. Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland.
  9. Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
  10. Proteome Research Centre, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
  11. Utrecht University and Netherlands Proteomics Centre, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
  12. Department of Analytical Chemistry and Food Chemistry, University of Vienna, 1090 Vienna, Austria.
  13. Bruker Daltonik GmbH, Bremen, Germany.
  14. Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.
  15. Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
  16. Molecular Sciences, Amgen Inc., Thousand Oaks, California, USA.
  17. Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90075, USA.
  18. Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
  19. The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, and The Molecular Biology Institute, and The Brain Research Institute, University of California, Los Angeles, California 90095, USA.
  20. Proteomics Research Laboratory, Tokyo Rikakikai Co., Tsukuba, Japan.
  21. Department of Biochemistry, Ghent University and Department of Medical Protein Research, Flanders Institute for Biotechnology, B-9000 Ghent, Belgium.
  22. Department of Medicine (Cardiology) and Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
  23. School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia.
  24. Serono Pharmaceutical Research Institute, 14, Chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland.
  25. The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, California 92037, USA.

Correspondence to: Chris F Taylor1,2 e-mail: chris.taylor@ebi.ac.uk.



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