Peptide Sequence Motif Analysis of Tandem MS Data with the SALSA Algorithm

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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.