Identification of cross-linked peptides from large sequence databases.
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.
Rinner
Oliver
O
Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.
Seebacher
Jan
J
Walzthoeni
Thomas
T
Mueller
Lukas N
LN
Beck
Martin
M
Schmidt
Alexander
A
Mueller
Markus
M
Aebersold
Ruedi
R
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
D003432:Cross-Linking Reagents; D010455:Peptides