title: Peptide sequence motif analysis of tandem MS data with the SALSA algorithm.
abstract: We have developed a pattern recognition algorithm called SALSA (scoring algorithm for spectral analysis) for the detection of specific features in tandem MS (MS-MS) spectra. Application of the SALSA algorithm to the detection of peptide MS-MS ion series enables identification of MS-MS spectra displaying characteristics of specific peptide sequences. SALSA analysis scores MS-MS spectra based on correspondence between theoretical ion series for peptide sequence motifs and actual MS-MS product ion series, regardless of their absolute positions on the m/z axis. Analyses of tryptic digests of bovine serum albumin (BSA) by LC-MS-MS followed by SALSA analysis detected MS-MS spectra for both unmodified and multiple modified forms of several BSA tryptic peptides. SALSA analysis of MS-MS data from mixtures of BSA and human serum albumin (HSA) tryptic digests indicated that ion series searches with BSA peptide sequence motifs identified MS-MS spectra for both BSA and closely related HSA peptides. Optimal discrimination between MS-MS spectra of variant peptide forms is achieved when the SALSA search criteria are optimized to the target peptide. Application of SALSA to LC-MS-MS proteome analysis will facilitate the characterization of modified and sequence variant proteins.
authors.affiliation: Southwest Environmental Health Sciences Center, College of Pharmacy and Department of Computer Science, The University of Arizona, Tucson 85721-0207, USA. liebler@pharmacy.arizona.edu
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
authors.forename: Beau T
authors.initials: BT
authors.lastname: Hansen
authors.forename: Sean W
authors.initials: SW
authors.lastname: Davey
authors.forename: Laura
authors.initials: L
authors.lastname: Tiscareno
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Mason
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000295:instrumentation / Q000379:methods*
chemical_list: D010455:Peptides