Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Identifieur interne : 000074 ( OpenAccess/Analysis ); précédent : 000073; suivant : 000075Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Auteurs : Christopher R. Kinsinger [États-Unis] ; James Apffel ; Mark Baker ; Xiaopeng Bian ; Christoph H. Borchers ; Ralph Bradshaw ; Mi-Youn Brusniak ; Daniel W. Chan ; Eric W. Deutsch ; Bruno Domon ; Jeff Gorman ; Rudolf Grimm ; William Hancock ; Henning Hermjakob ; David Horn ; Christie Hunter ; Patrik Kolar ; Hans-Joachim Kraus ; Hanno Langen ; Rune Linding ; Robert L. Moritz ; Gilbert S. Omenn ; Ron Orlando ; Akhilesh Pandey ; Peipei Ping ; Amir Rahbar ; Robert Rivers ; Sean L. Seymour ; Richard J. Simpson ; Douglas Slotta ; Richard D. Smith ; Stephen E. Stein ; David L. Tabb ; Danilo Tagle ; John R. Yates ; Henry RodriguezSource :
- PROTEOMICS [ 1615-9853 ] ; 2012-01.
English descriptors
- KwdEn :
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 research 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.
Url:
DOI: 10.1002/pmic.201100562
Affiliations:
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Kinsinger</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Apffel, James" sort="Apffel, James" uniqKey="Apffel J" first="James" last="Apffel">James Apffel</name></author><author><name sortKey="Baker, Mark" sort="Baker, Mark" uniqKey="Baker M" first="Mark" last="Baker">Mark Baker</name></author><author><name sortKey="Bian, Xiaopeng" sort="Bian, Xiaopeng" uniqKey="Bian X" first="Xiaopeng" last="Bian">Xiaopeng Bian</name></author><author><name sortKey="Borchers, Christoph H" sort="Borchers, Christoph H" uniqKey="Borchers C" first="Christoph H." last="Borchers">Christoph H. Borchers</name></author><author><name sortKey="Bradshaw, Ralph" sort="Bradshaw, Ralph" uniqKey="Bradshaw R" first="Ralph" last="Bradshaw">Ralph Bradshaw</name></author><author><name sortKey="Brusniak, Mi Oun" sort="Brusniak, Mi Oun" uniqKey="Brusniak M" first="Mi-Youn" last="Brusniak">Mi-Youn Brusniak</name></author><author><name sortKey="Chan, Daniel W" sort="Chan, Daniel W" uniqKey="Chan D" first="Daniel W." last="Chan">Daniel W. Chan</name></author><author><name sortKey="Deutsch, Eric W" sort="Deutsch, Eric W" uniqKey="Deutsch E" first="Eric W." last="Deutsch">Eric W. 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Moritz</name></author><author><name sortKey="Omenn, Gilbert S" sort="Omenn, Gilbert S" uniqKey="Omenn G" first="Gilbert S." last="Omenn">Gilbert S. Omenn</name></author><author><name sortKey="Orlando, Ron" sort="Orlando, Ron" uniqKey="Orlando R" first="Ron" last="Orlando">Ron Orlando</name></author><author><name sortKey="Pandey, Akhilesh" sort="Pandey, Akhilesh" uniqKey="Pandey A" first="Akhilesh" last="Pandey">Akhilesh Pandey</name></author><author><name sortKey="Ping, Peipei" sort="Ping, Peipei" uniqKey="Ping P" first="Peipei" last="Ping">Peipei Ping</name></author><author><name sortKey="Rahbar, Amir" sort="Rahbar, Amir" uniqKey="Rahbar A" first="Amir" last="Rahbar">Amir Rahbar</name></author><author><name sortKey="Rivers, Robert" sort="Rivers, Robert" uniqKey="Rivers R" first="Robert" last="Rivers">Robert Rivers</name></author><author><name sortKey="Seymour, Sean L" sort="Seymour, Sean L" uniqKey="Seymour S" first="Sean L." last="Seymour">Sean L. Seymour</name></author><author><name sortKey="Simpson, Richard J" sort="Simpson, Richard J" uniqKey="Simpson R" first="Richard J." last="Simpson">Richard J. Simpson</name></author><author><name sortKey="Slotta, Douglas" sort="Slotta, Douglas" uniqKey="Slotta D" first="Douglas" last="Slotta">Douglas Slotta</name></author><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D." last="Smith">Richard D. Smith</name></author><author><name sortKey="Stein, Stephen E" sort="Stein, Stephen E" uniqKey="Stein S" first="Stephen E." last="Stein">Stephen E. Stein</name></author><author><name sortKey="Tabb, David L" sort="Tabb, David L" uniqKey="Tabb D" first="David L." last="Tabb">David L. Tabb</name></author><author><name sortKey="Tagle, Danilo" sort="Tagle, Danilo" uniqKey="Tagle D" first="Danilo" last="Tagle">Danilo Tagle</name></author><author><name sortKey="Yates, John R" sort="Yates, John R" uniqKey="Yates J" first="John R." last="Yates">John R. Yates</name></author><author><name sortKey="Rodriguez, Henry" sort="Rodriguez, Henry" uniqKey="Rodriguez H" first="Henry" last="Rodriguez">Henry Rodriguez</name></author></analytic><monogr></monogr><series><title level="j">PROTEOMICS</title><title level="j" type="abbrev">Proteomics</title><idno type="ISSN">1615-9853</idno><idno type="eISSN">1615-9861</idno><imprint><publisher>WILEY‐VCH Verlag</publisher><pubPlace>Weinheim</pubPlace><date type="published" when="2012-01">2012-01</date><biblScope unit="volume">12</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="11">11</biblScope><biblScope unit="page" to="20">20</biblScope></imprint><idno type="ISSN">1615-9853</idno></series><idno type="istex">467B90253D1ADE9C82684C44728C9806A01BA91A</idno><idno type="DOI">10.1002/pmic.201100562</idno><idno type="ArticleID">PMIC201100562</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1615-9853</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amsterdam principles</term><term>Bioinformatics</term><term>Data quality</term><term>Metrics</term><term>Open access</term><term>Selected reaction monitoring</term><term>Standards</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><noCountry><name sortKey="Apffel, James" sort="Apffel, James" uniqKey="Apffel J" first="James" last="Apffel">James Apffel</name><name sortKey="Baker, Mark" sort="Baker, Mark" uniqKey="Baker M" first="Mark" last="Baker">Mark Baker</name><name sortKey="Bian, Xiaopeng" sort="Bian, Xiaopeng" uniqKey="Bian X" first="Xiaopeng" last="Bian">Xiaopeng Bian</name><name sortKey="Borchers, Christoph H" sort="Borchers, Christoph H" uniqKey="Borchers C" first="Christoph H." last="Borchers">Christoph H. Borchers</name><name sortKey="Bradshaw, Ralph" sort="Bradshaw, Ralph" uniqKey="Bradshaw R" first="Ralph" last="Bradshaw">Ralph Bradshaw</name><name sortKey="Brusniak, Mi Oun" sort="Brusniak, Mi Oun" uniqKey="Brusniak M" first="Mi-Youn" last="Brusniak">Mi-Youn Brusniak</name><name sortKey="Chan, Daniel W" sort="Chan, Daniel W" uniqKey="Chan D" first="Daniel W." last="Chan">Daniel W. Chan</name><name sortKey="Deutsch, Eric W" sort="Deutsch, Eric W" uniqKey="Deutsch E" first="Eric W." last="Deutsch">Eric W. Deutsch</name><name sortKey="Domon, Bruno" sort="Domon, Bruno" uniqKey="Domon B" first="Bruno" last="Domon">Bruno Domon</name><name sortKey="Gorman, Jeff" sort="Gorman, Jeff" uniqKey="Gorman J" first="Jeff" last="Gorman">Jeff Gorman</name><name sortKey="Grimm, Rudolf" sort="Grimm, Rudolf" uniqKey="Grimm R" first="Rudolf" last="Grimm">Rudolf Grimm</name><name sortKey="Hancock, William" sort="Hancock, William" uniqKey="Hancock W" first="William" last="Hancock">William Hancock</name><name sortKey="Hermjakob, Henning" sort="Hermjakob, Henning" uniqKey="Hermjakob H" first="Henning" last="Hermjakob">Henning Hermjakob</name><name sortKey="Horn, David" sort="Horn, David" uniqKey="Horn D" first="David" last="Horn">David Horn</name><name sortKey="Hunter, Christie" sort="Hunter, Christie" uniqKey="Hunter C" first="Christie" last="Hunter">Christie Hunter</name><name sortKey="Kolar, Patrik" sort="Kolar, Patrik" uniqKey="Kolar P" first="Patrik" last="Kolar">Patrik Kolar</name><name sortKey="Kraus, Hans Oachim" sort="Kraus, Hans Oachim" uniqKey="Kraus H" first="Hans-Joachim" last="Kraus">Hans-Joachim Kraus</name><name sortKey="Langen, Hanno" sort="Langen, Hanno" uniqKey="Langen H" first="Hanno" last="Langen">Hanno Langen</name><name sortKey="Linding, Rune" sort="Linding, Rune" uniqKey="Linding R" first="Rune" last="Linding">Rune Linding</name><name sortKey="Moritz, Robert L" sort="Moritz, Robert L" uniqKey="Moritz R" first="Robert L." last="Moritz">Robert L. Moritz</name><name sortKey="Omenn, Gilbert S" sort="Omenn, Gilbert S" uniqKey="Omenn G" first="Gilbert S." last="Omenn">Gilbert S. Omenn</name><name sortKey="Orlando, Ron" sort="Orlando, Ron" uniqKey="Orlando R" first="Ron" last="Orlando">Ron Orlando</name><name sortKey="Pandey, Akhilesh" sort="Pandey, Akhilesh" uniqKey="Pandey A" first="Akhilesh" last="Pandey">Akhilesh Pandey</name><name sortKey="Ping, Peipei" sort="Ping, Peipei" uniqKey="Ping P" first="Peipei" last="Ping">Peipei Ping</name><name sortKey="Rahbar, Amir" sort="Rahbar, Amir" uniqKey="Rahbar A" first="Amir" last="Rahbar">Amir Rahbar</name><name sortKey="Rivers, Robert" sort="Rivers, Robert" uniqKey="Rivers R" first="Robert" last="Rivers">Robert Rivers</name><name sortKey="Rodriguez, Henry" sort="Rodriguez, Henry" uniqKey="Rodriguez H" first="Henry" last="Rodriguez">Henry Rodriguez</name><name sortKey="Seymour, Sean L" sort="Seymour, Sean L" uniqKey="Seymour S" first="Sean L." last="Seymour">Sean L. Seymour</name><name sortKey="Simpson, Richard J" sort="Simpson, Richard J" uniqKey="Simpson R" first="Richard J." last="Simpson">Richard J. Simpson</name><name sortKey="Slotta, Douglas" sort="Slotta, Douglas" uniqKey="Slotta D" first="Douglas" last="Slotta">Douglas Slotta</name><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D." last="Smith">Richard D. Smith</name><name sortKey="Stein, Stephen E" sort="Stein, Stephen E" uniqKey="Stein S" first="Stephen E." last="Stein">Stephen E. Stein</name><name sortKey="Tabb, David L" sort="Tabb, David L" uniqKey="Tabb D" first="David L." last="Tabb">David L. Tabb</name><name sortKey="Tagle, Danilo" sort="Tagle, Danilo" uniqKey="Tagle D" first="Danilo" last="Tagle">Danilo Tagle</name><name sortKey="Yates, John R" sort="Yates, John R" uniqKey="Yates J" first="John R." last="Yates">John R. Yates</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="Kinsinger, Christopher R" sort="Kinsinger, Christopher R" uniqKey="Kinsinger C" first="Christopher R." last="Kinsinger">Christopher R. Kinsinger</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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