AustralieFrV1, Main, Exploration, bibRecord, 001D47

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Identifieur interne : 001D47 ( Main/Exploration ); précédent : 001D46; suivant : 001D48

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Auteurs : Eric W. Deutsch [États-Unis] ; Christopher M. Overall [Canada] ; Jennifer E. Van Eyk [États-Unis] ; Mark S. Baker [Australie] ; Young-Ki Paik [Corée du Sud] ; Susan T. Weintraub [États-Unis] ; Lydie Lane [Suisse] ; Lennart Martens [Belgique] ; Yves Vandenbrouck [France] ; Ulrike Kusebauch [États-Unis] ; William S. Hancock [États-Unis] ; Henning Hermjakob [Royaume-Uni, République populaire de Chine] ; Ruedi Aebersold [Suisse] ; Robert L. Moritz [États-Unis] ; Gilbert S. Omenn [États-Unis]

Source :

Journal of proteome research [ 1535-3893 ] ; 2016.

RBID : PMC:5096969

Descripteurs français

KwdFr :
- Bases de données de protéines, Bases de données factuelles, Humains, Protéome (), Protéomique (normes), Protéomique (organisation et administration), Recommandations comme sujet, Spectrométrie de masse (normes).
MESH :
- normes : Protéomique, Spectrométrie de masse.
- organisation et administration : Protéomique.
- Bases de données de protéines, Bases de données factuelles, Humains, Protéome, Recommandations comme sujet.

English descriptors

KwdEn :
- Databases, Factual, Databases, Protein, Guidelines as Topic, Humans, Mass Spectrometry (standards), Proteome (chemistry), Proteomics (organization & administration), Proteomics (standards).
MESH :
- chemical , chemistry : Proteome.
- organization & administration : Proteomics.
- standards : Mass Spectrometry, Proteomics.
- Databases, Factual, Databases, Protein, Guidelines as Topic, Humans.

Abstract

Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing fifteen essential points followed by two pages of expanded description of each. Here, we present an overview of the guidelines and provide an in-depth description of each of the fifteen elements to facilitate understanding of the intentions and rationale behind the guidelines, both for authors and for reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5096969

DOI: 10.1021/acs.jproteome.6b00392
PubMed: 27490519
PubMed Central: 5096969

Affiliations:

Le document en format XML

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<affiliation wicri:level="1"><nlm:aff id="A14">Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich</wicri:regionArea>
<wicri:noRegion>Zurich</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="A15">Faculty of Science, University of Zurich, 8006 Zurich, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Faculty of Science, University of Zurich, 8006 Zurich</wicri:regionArea>
<orgName type="university">Université de Zurich</orgName>
<placeName><settlement type="city">Zurich</settlement>
<region nuts="3" type="region">Canton de Zurich</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Moritz, Robert L" sort="Moritz, Robert L" uniqKey="Moritz R" first="Robert L." last="Moritz">Robert L. Moritz</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Institute for Systems Biology, Seattle, WA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Systems Biology, Seattle, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Omenn, Gilbert S" sort="Omenn, Gilbert S" uniqKey="Omenn G" first="Gilbert S." last="Omenn">Gilbert S. Omenn</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Institute for Systems Biology, Seattle, WA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Systems Biology, Seattle, WA</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A16">Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2218, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2218</wicri:regionArea>
<wicri:noRegion>48109-2218</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of proteome research</title>
<idno type="ISSN">1535-3893</idno>
<idno type="eISSN">1535-3907</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Factual</term>
<term>Databases, Protein</term>
<term>Guidelines as Topic</term>
<term>Humans</term>
<term>Mass Spectrometry (standards)</term>
<term>Proteome (chemistry)</term>
<term>Proteomics (organization & administration)</term>
<term>Proteomics (standards)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données de protéines</term>
<term>Bases de données factuelles</term>
<term>Humains</term>
<term>Protéome ()</term>
<term>Protéomique (normes)</term>
<term>Protéomique (organisation et administration)</term>
<term>Recommandations comme sujet</term>
<term>Spectrométrie de masse (normes)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteome</term>
</keywords>
<keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Protéomique</term>
<term>Spectrométrie de masse</term>
</keywords>
<keywords scheme="MESH" qualifier="organisation et administration" xml:lang="fr"><term>Protéomique</term>
</keywords>
<keywords scheme="MESH" qualifier="organization & administration" xml:lang="en"><term>Proteomics</term>
</keywords>
<keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Mass Spectrometry</term>
<term>Proteomics</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Databases, Factual</term>
<term>Databases, Protein</term>
<term>Guidelines as Topic</term>
<term>Humans</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Bases de données de protéines</term>
<term>Bases de données factuelles</term>
<term>Humains</term>
<term>Protéome</term>
<term>Recommandations comme sujet</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P1">Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guidelines that should be applied to all HPP data contributions. For submission of manuscripts reporting HPP protein identification results, the guidelines are presented as a one-page checklist containing fifteen essential points followed by two pages of expanded description of each. Here, we present an overview of the guidelines and provide an in-depth description of each of the fifteen elements to facilitate understanding of the intentions and rationale behind the guidelines, both for authors and for reviewers. Broadly, these guidelines provide specific directions regarding how HPP data are to be submitted to mass spectrometry data repositories, how error analysis should be presented, and how detection of novel proteins should be supported with additional confirmatory evidence. These guidelines, developed by the HPP community, are presented to the broader scientific community for further discussion.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Australie</li>
<li>Belgique</li>
<li>Canada</li>
<li>Corée du Sud</li>
<li>France</li>
<li>Royaume-Uni</li>
<li>République populaire de Chine</li>
<li>Suisse</li>
<li>États-Unis</li>
</country>
<region><li>Auvergne-Rhône-Alpes</li>
<li>Californie</li>
<li>Canton de Genève</li>
<li>Canton de Zurich</li>
<li>Massachusetts</li>
<li>Province de Flandre-Orientale</li>
<li>Rhône-Alpes</li>
<li>Région capitale de Séoul</li>
<li>Région flamande</li>
<li>Texas</li>
<li>Washington (État)</li>
</region>
<settlement><li>Gand</li>
<li>Genève</li>
<li>Grenoble</li>
<li>Pékin</li>
<li>Séoul</li>
<li>Zurich</li>
</settlement>
<orgName><li>Université Grenoble-Alpes</li>
<li>Université de Gand</li>
<li>Université de Genève</li>
<li>Université de Zurich</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Washington (État)"><name sortKey="Deutsch, Eric W" sort="Deutsch, Eric W" uniqKey="Deutsch E" first="Eric W." last="Deutsch">Eric W. Deutsch</name>
</region>
<name sortKey="Hancock, William S" sort="Hancock, William S" uniqKey="Hancock W" first="William S." last="Hancock">William S. Hancock</name>
<name sortKey="Kusebauch, Ulrike" sort="Kusebauch, Ulrike" uniqKey="Kusebauch U" first="Ulrike" last="Kusebauch">Ulrike Kusebauch</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="Omenn, Gilbert S" sort="Omenn, Gilbert S" uniqKey="Omenn G" first="Gilbert S." last="Omenn">Gilbert S. Omenn</name>
<name sortKey="Van Eyk, Jennifer E" sort="Van Eyk, Jennifer E" uniqKey="Van Eyk J" first="Jennifer E." last="Van Eyk">Jennifer E. Van Eyk</name>
<name sortKey="Weintraub, Susan T" sort="Weintraub, Susan T" uniqKey="Weintraub S" first="Susan T." last="Weintraub">Susan T. Weintraub</name>
</country>
<country name="Canada"><noRegion><name sortKey="Overall, Christopher M" sort="Overall, Christopher M" uniqKey="Overall C" first="Christopher M." last="Overall">Christopher M. Overall</name>
</noRegion>
</country>
<country name="Australie"><noRegion><name sortKey="Baker, Mark S" sort="Baker, Mark S" uniqKey="Baker M" first="Mark S." last="Baker">Mark S. Baker</name>
</noRegion>
</country>
<country name="Corée du Sud"><region name="Région capitale de Séoul"><name sortKey="Paik, Young Ki" sort="Paik, Young Ki" uniqKey="Paik Y" first="Young-Ki" last="Paik">Young-Ki Paik</name>
</region>
</country>
<country name="Suisse"><region name="Canton de Genève"><name sortKey="Lane, Lydie" sort="Lane, Lydie" uniqKey="Lane L" first="Lydie" last="Lane">Lydie Lane</name>
</region>
<name sortKey="Aebersold, Ruedi" sort="Aebersold, Ruedi" uniqKey="Aebersold R" first="Ruedi" last="Aebersold">Ruedi Aebersold</name>
<name sortKey="Aebersold, Ruedi" sort="Aebersold, Ruedi" uniqKey="Aebersold R" first="Ruedi" last="Aebersold">Ruedi Aebersold</name>
</country>
<country name="Belgique"><noRegion><name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name>
</noRegion>
<name sortKey="Martens, Lennart" sort="Martens, Lennart" uniqKey="Martens L" first="Lennart" last="Martens">Lennart Martens</name>
</country>
<country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Vandenbrouck, Yves" sort="Vandenbrouck, Yves" uniqKey="Vandenbrouck Y" first="Yves" last="Vandenbrouck">Yves Vandenbrouck</name>
</region>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Hermjakob, Henning" sort="Hermjakob, Henning" uniqKey="Hermjakob H" first="Henning" last="Hermjakob">Henning Hermjakob</name>
</noRegion>
</country>
<country name="République populaire de Chine"><noRegion><name sortKey="Hermjakob, Henning" sort="Hermjakob, Henning" uniqKey="Hermjakob H" first="Henning" last="Hermjakob">Henning Hermjakob</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

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