Journal
JOURNAL OF PROTEOME RESEARCH
Volume 9, Issue 5, Pages 2508-2515Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr9011816
Keywords
Cross-linking; mass spectrometry; protein-protein interaction; CXMS; software
Categories
Funding
- National Institutes of Health (NIH) [R33CA099139-01, 1S10RR023044-01, 1U54 AI57141-01]
- Swiss National Science Foundation (SNF) [PBLAA-119623, PA00P3_126252]
- Swiss National Science Foundation (SNF) [PA00P3_126252] Funding Source: Swiss National Science Foundation (SNF)
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We developed an informatic method to identify tandem mass spectra composed of chemically crosslinked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and XITandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.
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