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

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

doi:10.1038/nmeth.2103

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

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Citation

Walzthoeni, T., Claassen, M., Leitner, A., Herzog, F., Bohn, S., Förster, F., et al. (2012). False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nature Methods, 9(9), 901-903. doi:10.1038/nmeth.2103.

Cite as: https://hdl.handle.net/21.11116/0000-0006-EAE0-5

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.