title: Spectral Library Searching To Identify Cross-Linked Peptides.
abstract: Methods harnessing protein cross-linking and mass spectrometry (XL-MS) offer high-throughput means to identify protein-protein interactions (PPIs) and structural interfaces of protein complexes. Yet, specialized data dependent methods and search algorithms are often required to confidently assign peptide identifications to spectra. To improve the efficiency of matching high confidence spectra, we developed a spectral library based approach to search cross-linked peptide data derived from Protein Interaction Reporter (PIR) methods using the spectral library search algorithm, SpectraST. Spectral library matching of cross-linked peptide data from query spectra increased the absolute number of confident peptide relationships matched to spectra and thereby the number of PPIs identified. By matching library spectra from bona fide, previously established PIR-cross-linked peptide relationships, spectral library searching reduces the need for continued, complex mass spectrometric methods to identify peptide relationships, increases coverage of relationship identifications, and improves the accessibility of XL-MS technologies.
authors.forename: Devin K
authors.initials: DK
authors.lastname: Schweppe
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chavez
authors.forename: Arti T
authors.initials: AT
authors.lastname: Navare
authors.forename: Xia
authors.initials: X
authors.lastname: Wu
authors.forename: Bianca
authors.initials: B
authors.lastname: Ruiz
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.affiliation: Department of Chemical and Biomolcular Engineering, Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong, China.
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D000465:Algorithms; D057225:Data Mining; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000737:chemistry; D025941:Protein Interaction Mapping / Q000379:methods*
chemical_list: D010455:Peptides
keywords: XL-MS; protein cross-linking; spectral library