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Guidelines for reporting the use of mass spectrometry in proteomics

Nature Biotechnology volume 26, pages 860–861 (2008)Cite this article

To the editor:

A paper in last August's issue presented the overall Minimum Information about a Proteomics Experiment (MIAPE) reporting guidelines for the field of proteomics1. We would like to draw the community's attention to the MIAPE Mass Spectrometry (MIAPE-MS) module, which specifies the minimum information that should be provided when reporting the use of mass spectrometry in a proteomics experiment (Box 1). Developed through a joint effort between the Mass Spectrometry working group of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics community, MIAPE-MS constitutes one part of the MIAPE documentation system. It comprises a checklist of information that should be provided about mass spectrometry performed in the course of generating a data set that is submitted to a public repository or when such an experimental step is reported in a scientific publication (for instance, in the materials and methods section). MIAPE-MS specifies neither the format in which information should be transferred nor the structure of any repository or document. However, HUPO-PSI is not developing the MIAPE modules in isolation; several compatible data exchange standards are now well established and supported both by public databases and by data processing software in proteomics.

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References

  1. Taylor, C.F. et al. Nat. Biotechnol. 25, 887–893 (2007).

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Author information

Authors and Affiliations

  1. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, UK

    Chris F Taylor

  2. NERC Environmental Bioinformatics Centre, Mansfield Road, Oxford, OX1 3SR, UK

    Chris F Taylor

  3. Swiss Institute of Bioinformatics, Proteome Informatics Group, Rue Michel-Servet 1, Geneva 4, CH-1211, Switzerland

    Pierre-Alain Binz

  4. GeneBio SA, 25 Av. de Champel, Geneva, CH-1206, Switzerland

    Pierre-Alain Binz

  5. Institute for Molecular Systems Biology, ETH Zurich, HPT E 78, Wolfgang-Pauli-Str. 16, Zürich, 8093, Switzerland

    Ruedi Aebersold

  6. Nestlé Research Center, Nestec Ltd., Vers-chez-Les-Blanc, Lausanne 26, 1000, Switzerland

    Michel Affolter & Martin Kussmann

  7. Affimetrix, Inc., 3420 Central Expressway, Santa Clara, 95051, California, USA

    Robert Barkovich

  8. Institute for Systems Biology, 1441 N. 34th Street, Seattle, 98103, Washington, USA

    Eric W Deutsch

  9. Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, 95051, California, USA

    David M Horn

  10. Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, 95134, California, USA

    Andreas Hühmer

  11. Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QW, Cambridgeshire, UK

    Kathryn Lilley

  12. Bruker Daltonik GmbH, Bremen, Germany

    Marcus Macht

  13. Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany

    Matthias Mann

  14. Novartis Institutes for BioMedical Research, Developmental and Molecular Pathways, WSJ-088.702, Pathway Profiling, Basel, CH-4056, Switzerland

    Dieter Müller

  15. Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York, 10016, USA

    Thomas A Neubert

  16. Pathways, DECS, AstraZeneca, Alderley Park, Macclesfield, SK10 4TF, Cheshire, UK

    Janice Nickson

  17. Amgen Inc., Molecular Sciences, One Amgen Center Drive MS 38-3-A, Thousand Oaks, 91320-1799, California, USA

    Scott D Patterson

  18. Kratos Analytical (Shimadzu), Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK

    Roberto Raso

  19. Department of Chemistry & Biochemistry, University of Colorado, Boulder, 80309-0215, Colorado, USA

    Kathryn Resing

  20. Applied Biosystems, 850 Lincoln Centre Drive, Foster City, 94404, California, USA

    Sean L Seymour

  21. Proteomics Research Laboratory, Tokyo Rikakikai Co., Tsukuba, Japan

    Akira Tsugita

  22. Swiss Institute of Bioinformatics, Vital-IT group, Quartier Sorge – Bàtiment Génopole, Lausanne, CH-1015, Switzerland

    Ioannis Xenarios

  23. Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China

    Rong Zeng

  24. Indigo BioSystems, Inc., 111 Congressional Blvd., Suite 160, Carmel, 46032, Indiana, USA

    Randall K Julian Jr

Authors
  1. Chris F Taylor
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  2. Pierre-Alain Binz
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  3. Ruedi Aebersold
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  4. Michel Affolter
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  5. Robert Barkovich
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  6. Eric W Deutsch
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  7. David M Horn
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  8. Andreas Hühmer
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  9. Martin Kussmann
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  10. Kathryn Lilley
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  11. Marcus Macht
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  12. Matthias Mann
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  13. Dieter Müller
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  14. Thomas A Neubert
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  15. Janice Nickson
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  16. Scott D Patterson
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  17. Roberto Raso
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  18. Kathryn Resing
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  19. Sean L Seymour
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  20. Akira Tsugita
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  21. Ioannis Xenarios
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  22. Rong Zeng
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  23. Randall K Julian Jr
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Corresponding author

Correspondence to Pierre-Alain Binz.

Supplementary information

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SupplementaryTable 1, Guidelines (PDF 149 kb)

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Taylor, C., Binz, PA., Aebersold, R. et al. Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol 26, 860–861 (2008). https://doi.org/10.1038/nbt0808-860

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  • DOI: https://doi.org/10.1038/nbt0808-860

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