Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Identifieur interne : 000139 ( Istex/Corpus ); précédent : 000138; suivant : 000140Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Auteurs : Christopher R. Kinsinger ; 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 Iii ; Henry RodriguezSource :
- PROTEOMICS – Clinical Applications [ 1862-8346 ] ; 2011-12.
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 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.
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DOI: 10.1002/prca.201100097
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ISTEX:6194A85610BEB694433F6BA0F097DAAD5160BAC4Le document en format XML
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Appl.</title><idno type="ISSN">1862-8346</idno><idno type="eISSN">1862-8354</idno><imprint><publisher>WILEY‐VCH Verlag</publisher><pubPlace>Weinheim</pubPlace><date type="published" when="2011-12">2011-12</date><biblScope unit="volume">5</biblScope><biblScope unit="issue">11‐12</biblScope><biblScope unit="page" from="580">580</biblScope><biblScope unit="page" to="589">589</biblScope></imprint><idno type="ISSN">1862-8346</idno></series><idno type="istex">6194A85610BEB694433F6BA0F097DAAD5160BAC4</idno><idno type="DOI">10.1002/prca.201100097</idno><idno type="ArticleID">PRCA201100097</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1862-8346</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 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.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Christopher R. Kinsinger</name><affiliations><json:string>Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>James Apffel</name></json:item><json:item><name>Mark Baker</name></json:item><json:item><name>Xiaopeng Bian</name></json:item><json:item><name>Christoph H. Borchers</name></json:item><json:item><name>Ralph Bradshaw</name></json:item><json:item><name>Mi‐Youn Brusniak</name></json:item><json:item><name>Daniel W. Chan</name></json:item><json:item><name>Eric W. Deutsch</name></json:item><json:item><name>Bruno Domon</name></json:item><json:item><name>Jeff Gorman</name></json:item><json:item><name>Rudolf Grimm</name></json:item><json:item><name>William Hancock</name></json:item><json:item><name>Henning Hermjakob</name></json:item><json:item><name>David Horn</name></json:item><json:item><name>Christie Hunter</name></json:item><json:item><name>Patrik Kolar</name></json:item><json:item><name>Hans‐Joachim Kraus</name></json:item><json:item><name>Hanno Langen</name></json:item><json:item><name>Rune Linding</name></json:item><json:item><name>Robert L. Moritz</name></json:item><json:item><name>Gilbert S. Omenn</name></json:item><json:item><name>Ron Orlando</name></json:item><json:item><name>Akhilesh Pandey</name></json:item><json:item><name>Peipei Ping</name></json:item><json:item><name>Amir Rahbar</name></json:item><json:item><name>Robert Rivers</name></json:item><json:item><name>Sean L. Seymour</name></json:item><json:item><name>Richard J. 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Yates III</name></json:item><json:item><name>Henry Rodriguez</name></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Amsterdam principles</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Bioinformatics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Data quality</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Metrics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Open access</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Selected reaction monitoring</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Standards</value></json:item></subject><articleId><json:string>PRCA201100097</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>miscellaneous</json:string></originalGenre><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 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. 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KGaA, Weinheim</p></availability><date>2011</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)</title><author xml:id="author-1"><persName><forename type="first">Christopher R.</forename><surname>Kinsinger</surname></persName><note type="correspondence"><p>Correspondence: Office of Cancer Clinical Proteomics Research; National Cancer Institute; National Institutes of Health; 31 Center Drive, MSC 2580; Bethesda, Maryland 20892, USA +1‐301‐496‐7807</p></note><affiliation>Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA</affiliation></author><author xml:id="author-2"><persName><forename type="first">James</forename><surname>Apffel</surname></persName></author><author xml:id="author-3"><persName><forename type="first">Mark</forename><surname>Baker</surname></persName></author><author xml:id="author-4"><persName><forename type="first">Xiaopeng</forename><surname>Bian</surname></persName></author><author xml:id="author-5"><persName><forename type="first">Christoph H.</forename><surname>Borchers</surname></persName></author><author xml:id="author-6"><persName><forename type="first">Ralph</forename><surname>Bradshaw</surname></persName></author><author xml:id="author-7"><persName><forename type="first">Mi‐Youn</forename><surname>Brusniak</surname></persName></author><author xml:id="author-8"><persName><forename type="first">Daniel W.</forename><surname>Chan</surname></persName></author><author xml:id="author-9"><persName><forename type="first">Eric W.</forename><surname>Deutsch</surname></persName></author><author xml:id="author-10"><persName><forename type="first">Bruno</forename><surname>Domon</surname></persName></author><author xml:id="author-11"><persName><forename 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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. 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Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA<link href="#fn1"></link></unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en" type="author"><keyword xml:id="kwd1">Amsterdam principles</keyword><keyword xml:id="kwd2">Bioinformatics</keyword><keyword xml:id="kwd3">Data quality</keyword><keyword xml:id="kwd4">Metrics</keyword><keyword xml:id="kwd5">Open access</keyword><keyword xml:id="kwd6">Selected reaction monitoring</keyword><keyword xml:id="kwd7">Standards</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>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 <i>Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics,</i> 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.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><p>The remaining author affiliations are provided in the Addendum.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)</title></titleInfo><name type="personal"><namePart type="given">Christopher R.</namePart><namePart type="family">Kinsinger</namePart><affiliation>Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 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type="given">Ralph</namePart><namePart type="family">Bradshaw</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mi‐Youn</namePart><namePart type="family">Brusniak</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Daniel W.</namePart><namePart type="family">Chan</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Eric W.</namePart><namePart type="family">Deutsch</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bruno</namePart><namePart type="family">Domon</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jeff</namePart><namePart type="family">Gorman</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rudolf</namePart><namePart type="family">Grimm</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">William</namePart><namePart type="family">Hancock</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Henning</namePart><namePart type="family">Hermjakob</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Horn</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Christie</namePart><namePart type="family">Hunter</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Patrik</namePart><namePart type="family">Kolar</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hans‐Joachim</namePart><namePart type="family">Kraus</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hanno</namePart><namePart type="family">Langen</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rune</namePart><namePart type="family">Linding</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Robert L.</namePart><namePart type="family">Moritz</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Gilbert S.</namePart><namePart type="family">Omenn</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ron</namePart><namePart type="family">Orlando</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart 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type="given">Douglas</namePart><namePart type="family">Slotta</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Richard D.</namePart><namePart type="family">Smith</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Stephen E.</namePart><namePart type="family">Stein</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David L.</namePart><namePart type="family">Tabb</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Danilo</namePart><namePart type="family">Tagle</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">John R.</namePart><namePart type="family">Yates III</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Henry</namePart><namePart type="family">Rodriguez</namePart><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="miscellaneous"></genre><originInfo><publisher>WILEY‐VCH Verlag</publisher><place><placeTerm type="text">Weinheim</placeTerm></place><dateIssued encoding="w3cdtf">2011-12</dateIssued><dateCaptured encoding="w3cdtf">2011-10-27</dateCaptured><dateValid encoding="w3cdtf">2011-10-27</dateValid><copyrightDate encoding="w3cdtf">2011</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="tables">1</extent><extent unit="references">52</extent></physicalDescription><abstract 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 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.</abstract><subject lang="en"><genre>keywords</genre><topic>Amsterdam principles</topic><topic>Bioinformatics</topic><topic>Data quality</topic><topic>Metrics</topic><topic>Open access</topic><topic>Selected reaction monitoring</topic><topic>Standards</topic></subject><relatedItem type="host"><titleInfo><title>PROTEOMICS – Clinical Applications</title></titleInfo><titleInfo type="abbreviated"><title>Prot. Clin. Appl.</title></titleInfo><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>Standardisation & Guidelines</topic></subject><identifier type="ISSN">1862-8346</identifier><identifier type="eISSN">1862-8354</identifier><identifier type="DOI">10.1002/(ISSN)1862-8354</identifier><identifier type="PublisherID">PRCA</identifier><part><date>2011</date><detail type="volume"><caption>vol.</caption><number>5</number></detail><detail type="issue"><caption>no.</caption><number>11‐12</number></detail><extent unit="pages"><start>580</start><end>589</end><total>10</total></extent></part></relatedItem><identifier type="istex">6194A85610BEB694433F6BA0F097DAAD5160BAC4</identifier><identifier type="DOI">10.1002/prca.201100097</identifier><identifier type="ArticleID">PRCA201100097</identifier><accessCondition type="use and reproduction" contentType="copyright">Copyright © 2011 WILEY‐VCH Verlag GmbH & Co. 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