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Nat Methods. 2012 Sep;9(9):901-3. doi: 10.1038/nmeth.2103. Epub 2012 Jul 8.

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

Author information

1
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

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.

PMID:
22772729
DOI:
10.1038/nmeth.2103
[Indexed for MEDLINE]

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