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Updated: May 20, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
Published on: November 28, 2017
False discovery rate estimation for cross-linked peptides identified by mass spectrometry
Thomas Walzthoeni1, Manfred Claassen, Alexander Leitner
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
None:
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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