SALSA: A Hot New Tool for Protein Adduct Detection

Daniel C. Liebler, Ph.D.
University of Arizona, Tucson
R01ES10056 and P30ES06694

Background: Proteins are known to be targets of chemicals that induce toxicity and cancer. Recent developments in laboratory techniques and equipment have driven the growth of a new field of protein study known as proteomics. Proteomics is defined as the study of the entire protein complement encoded by a genome or the study of every protein produced by the genes of an organism. The integration of modern protein separation methods with mass spectrometry techniques provides powerful tools to analyze modifications of the proteome. The focus of these investigator's efforts are applying proteomics methods to studies of molecular toxicology and carcinogenesis.

Advance: The researchers have developed methods to identify protein targets of environmental chemicals by sequence analysis of peptides from damaged proteins. The analysis of adducted peptides reveals specific adduct-dependent features, which serve as indicators for modified peptides. These characteristics permit the identification of adducted peptides in the presence of unmodified peptides. They have developed a data analysis algorithm called SALSA (Scoring ALgorithm for Spectral Analysis), which identifies specific characteristics of modified peptides.

Implication: SALSA can automate the evaluation of thousands of protein spectra typically acquired in these analyses. The long-term objective of their research is to identify major protein targets of environmental chemicals to direct new research at understanding mechanisms of chemical toxicity. The greatest utility of SALSA will be in mining proteomic diversity and predicting toxicity of closely related and structurally similar chemicals.

Citation: Liebler DC, Hansen BT, Davey SW, Tiscareno L, Mason DE. Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal Chem. 2002 Jan 1;74(1):203-10.