Nature Methods
- 5, 315 - 318 (2008)
Published online: 9 March 2008; Corrected online: 27 June 2008 | doi:10.1038/nmeth.1192
There is a Corrigendum (August 2008) associated with this Brief Communication.
Identification of cross-linked peptides from large sequence databasesOliver Rinner1, Jan Seebacher2, Thomas Walzthoeni1, 3, Lukas N Mueller1, Martin Beck1, Alexander Schmidt1, 4, Markus Mueller1 & Ruedi Aebersold1, 2, 41
Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland. 2
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA. 3
University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria. 4
Faculty of Science, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
Correspondence should be addressed to Ruedi Aebersold aebersold@imsb.biol.ethz.ch NOTE: In the version of this Brief Communication initially published, an author name (Lukas Mueller) was incorrect. The correct author name is Lukas N Mueller. The error has been corrected in the HTML and PDF versions of the article.We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.
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