Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
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.
Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. kinsingc@mail.nih.gov
Christopher R
CR
Kinsinger
James
J
Apffel
Mark
M
Baker
Xiaopeng
X
Bian
Christoph H
CH
Borchers
Ralph
R
Bradshaw
Mi-Youn
MY
Brusniak
Daniel W
DW
Chan
Eric W
EW
Deutsch
Bruno
B
Domon
Jeff
J
Gorman
Rudolf
R
Grimm
William
W
Hancock
Henning
H
Hermjakob
David
D
Horn
Christie
C
Hunter
Patrik
P
Kolar
Hans-Joachim
HJ
Kraus
Hanno
H
Langen
Rune
R
Linding
Robert L
RL
Moritz
Gilbert S
GS
Omenn
Ron
R
Orlando
Akhilesh
A
Pandey
Peipei
P
Ping
Amir
A
Rahbar
Robert
R
Rivers
Sean L
SL
Seymour
Richard J
RJ
Simpson
Douglas
D
Slotta
Richard D
RD
Smith
Stephen E
SE
Stein
David L
DL
Tabb
Danilo
D
Tagle
John R
JR
Yates
Henry
H
Rodriguez
D022126:Access to Information; D019985:Benchmarking / Q000379:methods / Q000592:standards; D017408:Guidelines as Topic; D013058:Mass Spectrometry / Q000379:methods / Q000592:standards; D040901:Proteomics / Q000193:education / Q000379:methods / Q000592:standards; D012107:Research Design