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., United States

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

  • Author: Apffel, James, United States

    Agilent Research Laboratories, Santa Clara, United States

  • Author: Baker, Mark, United States

    Department of Chemistry and Biomolecular Sciences, Macquarie University, United States

  • Author: Bian, Xiaopeng, United States

    National Cancer Institute, National Institutes of Health, United States

  • Author: Borchers, Christoph H., Canada

    Genome BC Proteomics Centre, University of Victoria, Canada

  • Author: Bradshaw, Ralph, United States

    Mass Spectrometry Facility, University of California, United States

  • Author: Brusniak, Mi-Youn, United States

    Institute of Systems Biology, Seattle, United States

  • Author: Chan, Daniel W., United States

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

  • Author: Deutsch, Eric W., United States

    Institute for Systems Biology, Seattle, United States

  • Author: Domon, Bruno, Luxembourg

    Luxembourg Clinical Proteomics Center, CRP-Sante, Luxembourg

  • Author: Gorman, Jeff, Australia

    Protein Discovery Centre, Queensland Institute of Medical Research, Australia

  • Author: Grimm, Rudolf, United States

    Agilent Technologies, Santa Clara, United States

  • Author: Hancock, William, United States

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

  • Author: Hermjakob, Henning, United Kingdom

    Proteomics Services, European Bioinformatics Institute, Cambridge, United Kingdom

  • Author: Horn, David, United States

    Proteomics Software Strategic Marketing, Thermo Fisher Scientific, United States

  • Author: Hunter, Christie, United States

    AB SCIEX, Foster City, United States

  • Author: Kolar, Patrik, Belgium

    Directorate-General for Research, European Commission, Belgium

  • Author: Kraus, Hans-Joachim, Germany

    Wiley-VCH, Weinheim, Germany

  • Author: Langen, Hanno, Switzerland

    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., United States

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

  • Author: Omenn, Gilbert S., United States

    Center for Computational Medicine and Bioinformatics, University of Michigan, United States

  • Author: Orlando, Ron, United States

    Complex Carbohydrate Research Center, University of Georgia, United States

  • Author: Pandey, Akhilesh, United States

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

  • Author: Ping, Peipei, United States

    David Geffen School of Medicine, University of California, United States

  • Author: Rahbar, Amir, United States

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

  • Author: Rivers, Robert, United States

    AB SCIEX, Foster City, United States

  • Author: Seymour, Sean L., United States

    National Cancer Institute, National Institutes of Health, United States

  • Author: Simpson, Richard J., Australia

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

  • Author: Slotta, Douglas, United States

    Center for Biotechnology Information, National Institutes of Health, United States

  • Author: Smith, Richard D., United States

    Pacific Northwest National Laboratory, Richland, United States

  • Author: Stein, Stephen E., United States

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

  • Author: Tabb, David L., United States

    Vanderbilt-Ingram Cancer Center, United States

  • Author: Tagle, Danilo, United States

    National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States

  • Author: Yates, John R., III, United States

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

  • Author: Rodriguez, Henry, United States

    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
Journal number1
Pages11-20
ISSN1615-9853
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 10

Keywords

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