False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Thomas Walzthoeni; Manfred Claassen; Alexander Leitner; Franz Herzog; Stefan Bohn; Friedrich Förster; Martin Beck; Ruedi Aebersold

doi:10.1038/nmeth.2103

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Thomas Walzthoeni, Manfred Claassen, Alexander Leitner, Franz Herzog, Stefan Bohn, Friedrich Förster, Martin Beck, Ruedi Aebersold

Publikation: Beitrag in Fachzeitschrift › Artikel › Begutachtung

Abstract

The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.

Originalsprache	Englisch
Seiten (von - bis)	901-903
Seitenumfang	3
Fachzeitschrift	Nature Methods
Jahrgang	9
Ausgabenummer	9
DOIs	https://doi.org/10.1038/nmeth.2103
Publikationsstatus	Veröffentlicht - Sep. 2012
Extern publiziert	Ja

Forschungsfelder

Chemical Crosslinking
Mass spectrometry

IMC Forschungsschwerpunkte

Medical biotechnology

ÖFOS 2012 - Österreichischen Systematik der Wissenschaftszweige

106037 Proteomik
106041 Strukturbiologie
106044 Systembiologie

UN SDGs

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10.1038/nmeth.2103

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abstract = "The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.",

author = "Thomas Walzthoeni and Manfred Claassen and Alexander Leitner and Franz Herzog and Stefan Bohn and Friedrich F{\"o}rster and Martin Beck and Ruedi Aebersold",

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month = sep,

doi = "10.1038/nmeth.2103",

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T1 - False discovery rate estimation for cross-linked peptides identified by mass spectrometry

AU - Walzthoeni, Thomas

AU - Claassen, Manfred

AU - Leitner, Alexander

AU - Herzog, Franz

AU - Bohn, Stefan

AU - Förster, Friedrich

AU - Beck, Martin

AU - Aebersold, Ruedi

N1 - Funding Information: This work was supported by the European Union 7th Framework project PROSPECTS (Proteomics Specification in Space and Time, grant HEALTH-F4-2008-201648) and ERC advanced grant ‘Proteomics v3.0’ (grant no. 233226) of the European Union to R.A. We thank O. Rinner and A.I. Nesvizhskii for constructive discussions.

PY - 2012/9

Y1 - 2012/9

N2 - The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.

AB - The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.

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False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Abstract

Forschungsfelder

IMC Forschungsschwerpunkte

ÖFOS 2012 - Österreichischen Systematik der Wissenschaftszweige

UN SDGs

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