SEQUEST software

Figure 2.6 Automated analysis of BSA tryptic digest at 26 fmol pL 1 from position 3 on the device. MS-MS spectra were generated for the observed peaks. The MS-MS spectra for the labeled peaks were successfully matched to BSA by searching a protein sequence database using the Sequest software. The numbers indicate the measured m/z ratio and the charge state of the peptide ions.

In the case of the ESTMS-MS data, actual amino acid sequence can be deduced. This is possible due to the CID processes, which breaks the peptides further into amino acid ions. Each amino acid ion has a specific mass and by calculating masses of specific amino acid from the MS spectra, the exact sequence of the peptide and in turn the protein can be deduced. The workhorse of such analysis is a program called Sequest . Since the ESTMS-MS analysis provides information about the actual amino acid sequence, it is also useful to obtain information about protein modifications (such as phosphorylation) and toxicant-induced protein adducts. This has become even easier with the advent of new software tools and highly intelligent algorithms such as SALSA . 

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