A pattern recognition algorithm called SALSA (scoring algorithm for spectral analysis) has been developed to rapidly screen large numbers of peptide MS-MS spectra for fragmentation characteristics indicative of specific peptide modifications. The algorithm facilitates sensitive and specific detection of modified peptides at low abundance in an enzymatic protein digest. SALSA can simultaneously score multiple user-specified search criteria, including product ions, neutral losses, charged losses, and ion pairs that are diagnostic of specific peptide modifications. Application of SALSA to the detection of peptide adducts of the electrophiles dehydromonocrotaline, benzoquinone, and iodoacetic acid permitted their detection in a complex tryptic peptide digest mixture. SALSA provides superior detection of adducted peptides compared to conventional tandem MS precursor ion or neutral loss scans.
A proteome profiling approach was used to compare effects of two toxicants, 1,1-dicloroethylene (DCE) and diclofenac, which covalently adduct hepatic proteins. Bile was examined as a potential source of protein alterations since both toxicants target the hepatic biliary canaliculus. Bile was collected before and after toxicant treatment. Biliary proteins were separated by one-dimensional SDS-PAGE and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS-MS) with data-dependent scanning. Comprehensive analysis of biliary proteins was performed by using SEQUEST and BLAST database searching, in combination with de novo interpretation. Bile not subjected to tryptic digestion was analyzed for DCE metabolites. DCE treatment resulted in a marked increase in the overall number of biliary proteins, whereas few changes in the proteomic profile were apparent in bile after diclofenac treatment. This is consonant with prior observations of more profound effects of DCE on canalicular membrane integrity. LC-MS-MS analyses for DCE metabolites revealed the presence of S-carboxymethyl glutathione, S-(cysteinylacetyl)glutathione, and a product of the intramolecular rearrangement of the DCE metabolite, ClCH(2)COSG, not previously described in vivo. In addition, several S-carboxymethylated proteins were identified in bile from DCE-treated animals. This investigation has produced the first comprehensive baseline characterization of the content of the rat biliary proteome and the first documentation of alterations in the proteome of bile by toxicant treatment. In addition, the results provide direct in vivo evidence for DCE metabolic routes proposed in the formation of covalent adducts.
Dichloroethylene (DCE) is a hepatotoxin that undergoes cytochrome P450-catalyzed bioactivation in hepatocytes to form 2-chloroacetyl chloride and 1,1-dichloroethylene oxide. 2-Chloroacetyl chloride reacts with nucleophilic residues and with N-terminal amines to produce 2-chloroacetylated residues and with glutathione to form the reactive electrophile S-(2-chloroacetyl)glutathione (ClCH(2)COSG), which, in turn, is capable of sulfhydryl alkylation. 1,1-DCE oxide can bind to cysteine sulfhydryl groups and subsequently hydrolyze to form an S-carboxymethylated cysteine residue. S-Carboxymethylated, 2-chloroacetylated, and GSCOCH(2)-S-Cys-peptide adducts of model cysteine-containing peptides were synthesized, and their fragmentation patterns were characterized by electrospray tandem mass spectrometry. Synthesis of GSCOCH(2)-S-Cys-peptide adducts was achieved via a novel tert-butoxycarbonyl (tBOC) derivative of ClCH(2)COSG. CID of GSCOCH(2)-S-Cys-peptide adducts resulted in product ions and neutral losses indicative of the GSCOCH(2)-S-Cys moiety as well fragment ion pairs in the b- and y-ion series corresponding to the modified cysteine residue. S-Carboxymethylated peptides exhibited only a characteristic b- or y-series ion pair separated by 161 Da, corresponding to cysteine + CH(2)COOH. CID of 2-chloroacetylated peptides showed neutral losses of 36 (HCl), 78 (HCOCH(2)Cl), 96 (HCOCH(2)Cl + H(2)O), and 114 Da (HCOCH(2)Cl + 2H(2)O). Combinations of characteristic fragment ions, neutral losses, and ion pairs thus are characteristic for DCE-derived adducts. These features can be used in an MS/MS data reduction algorithm for the selective identification of protein targets of DCE metabolites.
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