title: Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs.
abstract: Mass spectrometric identification of cross-linked peptides can provide valuable information about the structure of protein complexes. We describe a straightforward database search scheme that identifies and assigns statistical confidence estimates to spectra from cross-linked peptides. The method is well suited to targeted analysis of a single protein complex, without requiring an isotope labeling strategy. Our approach uses a SEQUEST-style search procedure in which the database is comprised of a mixture of single peptides with and without linkers attached and cross-linked products. In contrast to several previous approaches, we generate theoretical spectra that account for all of the expected peaks from a cross-linked product, and we employ an empirical curve-fitting procedure to estimate statistical confidence measures. We show that our fully automated procedure successfully reidentifies spectra from a previous study, and we provide evidence that our statistical confidence estimates are accurate.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: McIlwain
authors.forename: Paul
authors.initials: P
authors.lastname: Draghicescu
authors.forename: Pragya
authors.initials: P
authors.lastname: Singh
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D000595:Amino Acid Sequence; D019392:Cytochrome P-450 CYP2E1 / Q000737:chemistry / Q000378:metabolism; D015786:Cytochromes b5 / Q000737:chemistry / Q000378:metabolism; D030562:Databases, Protein; D004926:Escherichia coli; D006801:Humans; D016014:Linear Models; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D010455:Peptides; D011994:Recombinant Proteins; D015786:Cytochromes b5; D019392:Cytochrome P-450 CYP2E1