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Peptide sequence motif analysis of tandem MS data with the SALSA algorithm.

Daniel C Liebler·Beau T Hansen·Sean W Davey·Laura Tiscareno·Daniel E Mason
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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.

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AlgorithmsAmino Acid MotifsAnimalsHumansMass SpectrometryPeptidesSequence Analysis, ProteinJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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Daniel C Liebler, Beau T Hansen, Sean W Davey, Laura Tiscareno, Daniel E Mason. 2002-01-01. Peptide sequence motif analysis of tandem MS data with the SALSA algorithm.. https://doi.org/10.1021/ac0155512

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