Figure 1. The different steps involved in chemical Edman sequencing. ATZ: anilinothiazolinone; PITC: phenylisothiocyanate; PTC: phenylthiocarbamyl; PTH: phenylthiohydantoin.

Figure 2. Example of an MALDI-TOF-MS peptide mass fingerprint obtained from a tryptic digest of Escherichia coli malate dehydrogenase isolated by 2D-PAGE. Tryptic peptides belonging to the identified protein are indicated by their masses. T indicates trypsin autodigestion products.

Figure 3. Quadrupole TOF MS/MS spectrum of a peptide obtained after RP-HPLC separation of the tryptic digestion of an affinity-isolated protein. The doubly charged ion of a peptide with mass 1351.63 Da was selected automatically by the mass spectrometer and fragmented by collision-activated dissociation. The obtained MS/MS spectrum was used automatically for peptide identification by the Mascot search algorithm (Matrix Science). The amino acid sequence  NH₂-T-A-S-G-S-S-V-T-S-L-E-G-T-R-COOH (in single-letter code) was returned as the best matching peptide and belongs to the n-myc downstream regulated gene 1 protein (GenBank accession number Q62433). After automatic identification, the MS/MS spectrum was scanned manually for the presence of y-type fragment ions, through which a large portion of the proposed amino acid sequence could be deduced.