title: Identification of cross-linked peptides from large sequence databases.
abstract: 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.
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rinner
authors.forename: Jan
authors.initials: J
authors.lastname: Seebacher
authors.forename: Thomas
authors.initials: T
authors.lastname: Walzthoeni
authors.forename: Lukas N
authors.initials: LN
authors.lastname: Mueller
authors.forename: Martin
authors.initials: M
authors.lastname: Beck
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.forename: Markus
authors.initials: M
authors.lastname: Mueller
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003432:Cross-Linking Reagents / Q000032:analysis* / Q000737:chemistry; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D013058:Mass Spectrometry; D008958:Models, Molecular; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011487:Protein Conformation; D012680:Sensitivity and Specificity
chemical_list: D003432:Cross-Linking Reagents; D010455:Peptides