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

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Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	901-3
Number of pages	3
Journal	Nature Methods
Volume	9
Issue number	9
DOIs	https://doi.org/10.1038/nmeth.2103
Publication status	Published - Sept 2012
Externally published	Yes

Keywords

Algorithms
Automation
Cross-Linking Reagents
Data Interpretation, Statistical
Databases, Protein
False Positive Reactions
Mass Spectrometry
Models, Molecular
Peptides
Protein Conformation
Proteomics
Software

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10.1038/nmeth.2103

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title = "False discovery rate estimation for cross-linked peptides identified by mass spectrometry",

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.",

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year = "2012",

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doi = "10.1038/nmeth.2103",

language = "English",

volume = "9",

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journal = "Nature Methods",

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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

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.

KW - Algorithms

KW - Automation

KW - Cross-Linking Reagents

KW - Data Interpretation, Statistical

KW - Databases, Protein

KW - False Positive Reactions

KW - Mass Spectrometry

KW - Models, Molecular

KW - Peptides

KW - Protein Conformation

KW - Proteomics

KW - Software

U2 - 10.1038/nmeth.2103

DO - 10.1038/nmeth.2103

M3 - Article

C2 - 22772729

SN - 1548-7091

VL - 9

SP - 901

EP - 903

JO - Nature Methods

JF - Nature Methods

IS - 9

ER -

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

Abstract

Keywords

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