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Nature Research, Nature Methods, 4(5), p. 315-318, 2008

DOI: 10.1038/nmeth.1192

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Identification of cross-linked peptides from large sequence databases

Journal article published in 2008 by Oliver Rinner, Jan Seebacher, Thomas Walzthoeni, Lukas N. Mueller, Martin Beck ORCID, Alexander Schmidt, Markus Mueller, Ruedi Aebersold
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases. The advance was achieved by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics, and a novel search engine called xQuest. This software reduces the search space by an upstream candidatepeptide search before the recombination step; we show that xQuest can identify cross-linked peptides from a total E. coli lysate with an unrestricted database search.