SALSA: A pattern recognition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LC-MS-MS analyses

A pattern recognition algorithm called SALSA (scoring algorithm for spectra l analysis) has been developed to rapidly screen large numbers of peptide M S-MS spectra for fragmentation characteristics indicative of specific pepti de modifications. The algorithm facilitates sensitive and specific detectio n of modified peptides at low abundance in an enzymatic protein digest. SAL SA can simultaneously score multiple user-specified search criteria, includ ing product ions, neutral losses, charged losses, and ion pairs that are di agnostic of specific peptide modifications. Application of SALSA to the det ection of peptide adducts of the electrophiles dehydromonocrotaline, benzoq uinone, and iodoacetic acid permitted their detection in a complex tryptic peptide digest mixture, SALSA provides superior detection of adducted pepti des compared to conventional tandem MS precursor ion or neutral loss scans.