Standardisation & Guidelines

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)

  1. Christopher R. Kinsinger*,
  2. James Apffel,
  3. Mark Baker,
  4. Xiaopeng Bian,
  5. Christoph H. Borchers,
  6. Ralph Bradshaw,
  7. Mi-Youn Brusniak,
  8. Daniel W. Chan,
  9. Eric W. Deutsch,
  10. Bruno Domon,
  11. Jeff Gorman,
  12. Rudolf Grimm,
  13. William Hancock,
  14. Henning Hermjakob,
  15. David Horn,
  16. Christie Hunter,
  17. Patrik Kolar,
  18. Hans-Joachim Kraus,
  19. Hanno Langen,
  20. Rune Linding,
  21. Robert L. Moritz,
  22. Gilbert S. Omenn,
  23. Ron Orlando,
  24. Akhilesh Pandey,
  25. Peipei Ping,
  26. Amir Rahbar,
  27. Robert Rivers,
  28. Sean L. Seymour,
  29. Richard J. Simpson,
  30. Douglas Slotta,
  31. Richard D. Smith,
  32. Stephen E. Stein,
  33. David L. Tabb,
  34. Danilo Tagle,
  35. John R. Yates III,
  36. Henry Rodriguez

Article first published online: 28 DEC 2011

DOI: 10.1002/prca.201100097

Issue

PROTEOMICS - Clinical Applications

PROTEOMICS - Clinical Applications

Volume 5, Issue 11-12, pages 580–589, December 2011

Additional Information

How to Cite

Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R., Brusniak, M.-Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., Hancock, W., Hermjakob, H., Horn, D., Hunter, C., Kolar, P., Kraus, H.-J., Langen, H., Linding, R., Moritz, R. L., Omenn, G. S., Orlando, R., Pandey, A., Ping, P., Rahbar, A., Rivers, R., Seymour, S. L., Simpson, R. J., Slotta, D., Smith, R. D., Stein, S. E., Tabb, D. L., Tagle, D., Yates, J. R. and Rodriguez, H. (2011), Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Prot. Clin. Appl., 5: 580–589. doi: 10.1002/prca.201100097

Author Information

  1. Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA†

*Office of Cancer Clinical Proteomics Research; National Cancer Institute; National Institutes of Health; 31 Center Drive, MSC 2580; Bethesda, Maryland 20892, USA Fax: +1-301-496-7807

Publication History

  1. Issue published online: 28 DEC 2011
  2. Article first published online: 28 DEC 2011
  3. Manuscript Received: 27 OCT 2011
  4. Manuscript Accepted: 27 OCT 2011

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Keywords:

  • Amsterdam principles;
  • Bioinformatics;
  • Data quality;
  • Metrics;
  • Open access;
  • Selected reaction monitoring;
  • Standards

Abstract

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.

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