Automatic Poisson peak harvesting for high throughput protein identification

High throughput identification of proteins by peptide mass fingerprinting r equires an efficient means of picking peaks from mass spectra. Mere, we rep ort the development of a peak harvester to automatically pick monoisotopic peaks from spectra generated on matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometers. The peak harvester uses adv anced mathematical morphology and watershed algorithms to first process spe ctra to stick representations. Subsequently, Poisson modelling is applied t o determine which peak in an isotopically resolved group represents the mon oisotopic mass of a peptide. We illustrate the features of the peak harvest er with mass spectra of standard peptides, digests of gel-separated bovine serum albumin, and with Escherictia coli proteins prepared by two-dimension al polyacrylamide gel electrophoresis. In all cases, the peak harvester pro ved effective in its ability to pick similar monoisotopic peaks as an exper ienced human operator, and also proved effective in the identification of m onoisotopic masses in cases where isotopic distributions of peptides were o verlapping. The peak harvester can be operated in an interactive mode, or c an be completely automated and linked through to peptide mass fingerprintin g protein identification tools to achieve high throughput automated protein identification.