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

被引：15

作者：

Kinsinger, Christopher R. ^{[1
]}

Apffel, James ^{[2
]}

Baker, Mark ^{[3
]}

Bian, Xiaopeng ^{[4
]}

Borchers, Christoph H. ^{[5
]}

Bradshaw, Ralph ^{[6
]}

Brusniak, Mi-Youn ^{[7
]}

Chan, Daniel W. ^{[8
]}

Deutsch, Eric W. ^{[9
]}

Domon, Bruno ^{[10
]}

Gorman, Jeff ^{[11
]}

Grimm, Rudolf ^{[12
]}

Hancock, William ^{[13
]}

Hermjakob, Henning ^{[14
]}

Horn, David ^{[15
]}

Hunter, Christie ^{[16
]}

Kolar, Patrik ^{[17
]}

Kraus, Hans-Joachim ^{[18
]}

Langen, Hanno ^{[19
]}

Linding, Rune ^{[20
]}

Moritz, Robert L. ^{[21
]}

Omenn, Gilbert S. ^{[22
]}

Orlando, Ron ^{[23
]}

Pandey, Akhilesh ^{[24
]}

Ping, Peipei ^{[25
]}

Rahbar, Amir ^{[1
]}

Rivers, Robert ^{[16
]}

Seymour, Sean L. ^{[26
]}

Simpson, Richard J. ^{[27
]}

Slotta, Douglas ^{[28
]}

Smith, Richard D. ^{[29
]}

Stein, Stephen E. ^{[30
]}

Tabb, David L. ^{[31
]}

Tagle, Danilo ^{[32
]}

Yates, John R., III ^{[33
]}

Rodriguez, Henry ^{[1
]}

机构：

[1] NCI, Off Canc Clin Prote Res, NIH, 31 Ctr Dr,MSC 2580, Bethesda, MD 20892 USA

[2] Agilent Res Labs, Santa Clara, CA USA

[3] Macquarie Univ, Dept Chem & Biomol Sci, Sydney, NSW, Australia

[4] NCI, Ctr Bioinformat & Informat Technol, NIH, Bethesda, MD USA

[5] Univ Victoria, Genome BC Prote Ctr, Victoria, BC, Canada

[6] Univ Calif San Francisco, Mass Spectrometry Facil, San Francisco, CA USA

[7] Inst Syst Biol, Seattle, WA USA

[8] Johns Hopkins Univ, Sch Med, Dept Pathol, Baltimore, MD USA

[9] Inst Syst Biol, Seattle, WA USA

[10] CRP Sante, Luxembourg Clin Prote Ctr, L-1445 Strassen, Luxembourg

[11] Queensland Inst Med Res, Prot Discovery Ctr, Herston, Qld, Australia

[12] Agilent Technol, Santa Clara, CA USA

[13] Northeastern Univ, Dept Chem & Chem Biol, Boston, MA USA

[14] European Bioinformat Inst, Prote Serv, Cambridge, England

[15] Thermo Fisher Sci, Prote Software Strateg Mkt, San Jose, CA USA

[16] AB SCIEX, Foster City, CA USA

[17] Commiss European Communities, Directorate Gen Res, Brussels, Belgium

[18] Wiley VCH, Weinheim, Germany

[19] Hoffmann La Roche AG, Exploratory Biomarkers, Basel, Switzerland

[20] Tech Univ Denmark DTU, Cellular Signal Integrat Grp C SIG, Ctr Biol Sequence Anal CBS, Dept Syst Biol, Lyngby, Denmark

[21] Inst Syst Biol, Cellular & Mol Log Unit, Seattle, WA USA

[22] Univ Michigan, Ctr Computat Med & Bioinformat, Ann Arbor, MI USA

[23] Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA USA

[24] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD USA

[25] Univ Calif Los Angeles, David Geffen Sch Med, Los Angeles, CA USA

[26] NCI, Small Business Dev Ctr, NIH, Bethesda, MD USA

[27] La Trobe Univ, La Trobe Inst Mol Sci, Bundoora, Vic, Australia

[28] NIH, Natl Ctr Biotechnol Informat, Bethesda, MD USA

[29] Pacific NW Natl Lab, Richland, WA USA

[30] NIST, Chem Reference Data Grp, Gaithersburg, MD USA

[31] Vanderbilt Ingram Canc Ctr, Nashville, TN USA

[32] Natl Inst Neurol Disorders & Stroke, NIH, Bethesda, MD USA

[33] Scripps Res Inst, La Jolla, CA USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2012年 / 11卷 / 02期

关键词：

selected reaction monitoring; bioinformatics; data quality; metrics; open access; Amsterdam Principles; standards; PROTEIN IDENTIFICATION DATA; PEPTIDE IDENTIFICATION; CLINICAL PROTEOMICS; MINIMUM INFORMATION; STATISTICAL-MODEL; GUIDELINES; RESOURCE; REPRODUCIBILITY; PERFORMANCE; VALIDATION;

D O I：

10.1021/pr201071t

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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: (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.

引用

页码：1412 / 1419

页数：8

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