Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)
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 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 search community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon 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, thismore »
- Authors:
- more »
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1034581
- Report Number(s):
- PNNL-SA-85425
400412000; TRN: US201203%%631
- DOE Contract Number:
- AC05-76RL01830
- Resource Type:
- Journal Article
- Journal Name:
- Proteomics - Clinical Applications
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 11-12
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; DATA PROCESSING; MASS SPECTROSCOPY; METRICS; NEOPLASMS; PROTEINS; QUALITY ASSURANCE; RECOMMENDATIONS; TRAINING; Amsterdam principles; Bioinformatics; Data quality; Metrics; Open access; Selected reaction monitoring
Citation Formats
Kingsinger, Christopher R, Apffel, James, Baker, Mark S, Bian, Xiaopeng, Borchers, Christoph H, Bradshaw, Ralph A, Brusniak, Mi-Youn, Chan, Daniel W, Deutsch, Eric W, Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William S, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L, Omenn, Gilbert S, Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L, Simpson, Richard J, Slotta, Douglas, Smith, Richard D, Stein, Stephen E, Tabb, David L, Tagle, Danilo, Yates, John R, and Rodriguez, Henry. Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles). United States: N. p., 2011.
Web. doi:10.1002/prca.201100097.
Kingsinger, Christopher R, Apffel, James, Baker, Mark S, Bian, Xiaopeng, Borchers, Christoph H, Bradshaw, Ralph A, Brusniak, Mi-Youn, Chan, Daniel W, Deutsch, Eric W, Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William S, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L, Omenn, Gilbert S, Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L, Simpson, Richard J, Slotta, Douglas, Smith, Richard D, Stein, Stephen E, Tabb, David L, Tagle, Danilo, Yates, John R, & Rodriguez, Henry. Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles). United States. https://doi.org/10.1002/prca.201100097
Kingsinger, Christopher R, Apffel, James, Baker, Mark S, Bian, Xiaopeng, Borchers, Christoph H, Bradshaw, Ralph A, Brusniak, Mi-Youn, Chan, Daniel W, Deutsch, Eric W, Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William S, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L, Omenn, Gilbert S, Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L, Simpson, Richard J, Slotta, Douglas, Smith, Richard D, Stein, Stephen E, Tabb, David L, Tagle, Danilo, Yates, John R, and Rodriguez, Henry. 2011.
"Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)". United States. https://doi.org/10.1002/prca.201100097.
@article{osti_1034581,
title = {Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)},
author = {Kingsinger, Christopher R and Apffel, James and Baker, Mark S and Bian, Xiaopeng and Borchers, Christoph H and Bradshaw, Ralph A and Brusniak, Mi-Youn and Chan, Daniel W and Deutsch, Eric W and Domon, Bruno and Gorman, Jeff and Grimm, Rudolf and Hancock, William S and Hermjakob, Henning and Horn, David and Hunter, Christie and Kolar, Patrik and Kraus, Hans-Joachim and Langen, Hanno and Linding, Rune and Moritz, Robert L and Omenn, Gilbert S and Orlando, Ron and Pandey, Akhilesh and Ping, Peipei and Rahbar, Amir and Rivers, Robert and Seymour, Sean L and Simpson, Richard J and Slotta, Douglas and Smith, Richard D and Stein, Stephen E and Tabb, David L and Tagle, Danilo and Yates, John R and Rodriguez, Henry},
abstractNote = {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 search community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon 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.},
doi = {10.1002/prca.201100097},
url = {https://www.osti.gov/biblio/1034581},
journal = {Proteomics - Clinical Applications},
number = 11-12,
volume = 5,
place = {United States},
year = {Thu Dec 01 00:00:00 EST 2011},
month = {Thu Dec 01 00:00:00 EST 2011}
}