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 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.
Highlights
On September 18, 2010, members of the international proteomics community met for a one-day workshop in Sydney, University, Baltimore, Maryland 21231, the David Geffen School of Medicine, University of California, Los Angeles, California 90095, the Small Business Development Center, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, the Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, AB Sciex, Foster City, California 94404, La Trobe Institute for Molecular
That was convened by the National Cancer Institute (NCI)1 of the United States National Institutes of Health
This workshop was held to address the lack of widely implementable policies governing the adoption and use of quality metrics for open access proteomic data, concerning tandem mass spectrometry data used to identify and quantify proteins based on fragmentation of peptide ions
Summary
Editors from the journal Molecular and Cellular Proteomics (MCP) recognized the need for manuscript submission guidelines to assist reviewers and readers of the paper in understanding the methods by which the authors acquired, processed, and analyzed their data [4] This was followed by an expanded set of guidelines developed by an invited group of participants that met in Paris, France in 2005 [5, 6]. A list of differentially expressed proteins, enriched networks, or biomarker candidates connects to derived information through higher level analyses conducted in statistical or systems biology tools This meeting report discusses the basic principles underlying data quality metrics in proteomics and the challenges to develop and implement these principles. Its purpose is to serve as a focus of discussion and action that will guide the continuing commitment of the field to conduct high quality research and to make the product of that research useful to the global research community
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