Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

Publication: Research - peer-reviewJournal article – Annual report year: 2012

  • Author: Kinsinger, Christopher R.

    Office of Cancer Clinical Proteomics Research, National Cancer Institute, United States

  • Author: Apffel, James

    Agilent Research Laboratories, Santa Clara, United States

  • Author: Baker, Mark

    Macquarie University, United States

  • Author: Bian, Xiaopeng

    National Institutes of Health, United States

  • Author: Borchers, Christoph H.

    University of Victoria, Canada

  • Author: Bradshaw, Ralph

    University of California, United States

  • Author: Brusniak, Mi-Youn

    Institute of Systems Biology, Seattle, United States

  • Author: Chan, Daniel W.

    Department of Pathology, Johns Hopkins University School of Medicine, United States

  • Author: Deutsch, Eric W.

    Institute for Systems Biology, Seattle, United States

  • Author: Domon, Bruno

    Luxembourg Clinical Proteomics Center, CRP-Sante, Luxembourg

  • Author: Gorman, Jeff

    QIMR Berghofer Medical Research Institute, Australia

  • Author: Grimm, Rudolf

    Agilent Technologies, Santa Clara, United States

  • Author: Hancock, William

    Department of Chemistry and Chemical Biology, Northeastern University, United States

  • Author: Hermjakob, Henning

    European Bioinformatics Institute, United Kingdom

  • Author: Horn, David

    Proteomics Software Strategic Marketing, Thermo Fisher Scientific, United States

  • Author: Hunter, Christie

    AB SCIEX, Foster City, United States

  • Author: Kolar, Patrik

    Directorate-General for Research, European Commission, Belgium

  • Author: Kraus, Hans-Joachim

    Wiley-VCH, Weinheim, Germany

  • Author: Langen, Hanno

    Exploratory Biomarkers, Hoffmann-La Roche, Switzerland

  • Author: Linding, Rune

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Anker Engelunds Vej, 2800, Kgs. Lyngby, Denmark

  • Author: Moritz, Robert L.

    Cellular and Molecular Logic Unit, Institute of Systems Biology, Seattle, United States

  • Author: Omenn, Gilbert S.

    University of Michigan, United States

  • Author: Orlando, Ron

    Complex Carbohydrate Research Center, University of Georgia, United States

  • Author: Pandey, Akhilesh

    McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, United States

  • Author: Ping, Peipei

    University of California, United States

  • Author: Rahbar, Amir

    Office of Cancer Clinical Proteomics Research, National Cancer Institute, United States

  • Author: Rivers, Robert

    AB SCIEX, Foster City, United States

  • Author: Seymour, Sean L.

    National Institutes of Health, United States

  • Author: Simpson, Richard J.

    La Trobe institute for Molecular Science, L Trobe University, Australia

  • Author: Slotta, Douglas

    National Institutes of Health, United States

  • Author: Smith, Richard D.

    Pacific Northwest National Laboratory, United States

  • Author: Stein, Stephen E.

    Chemical Reference Data Group, National Institute of Standards and Technology, United States

  • Author: Tabb, David L.

    Vanderbilt-Ingram Cancer Center, United States

  • Author: Tagle, Danilo

    National Institutes of Health, United States

  • Author: Yates, John R., III

    The Scripps Research Institute, The Scripps Research Institute, United States

  • Author: Rodriguez, Henry

    Office of Cancer Clinical Proteomics Research, National Cancer Institute, United States

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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 United States National Cancer Institute 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: 1) an evolving list of comprehensive quality metrics and 2) 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 the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications 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.
Original languageEnglish
JournalProteomics
Publication date2012
Volume12
Issue1
Pages11-20
ISSN1615-9853
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 13

Keywords

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