Figure 3.

Bioinformatics approaches for MS-based peptide identification. Two categories of approaches are distinct: the database search approach depends on generating theoretical spectra in silico from protein sequences in a database and querying experimental spectra against those to find the closest matches; the de novo tag approach infers peptide sequence directly from experimental MS/MS data by calculating mass shifts between series of peptide fragment ions, and then aligns the tag to protein in the database. Unassigned de novo tags can be used to interrogate EST depositories or databases of homologous species.