What enzymes should I use to digest the protein, in order to use PEAKS to interpret the MS/MS data?
Answer. The most popular enzyme for digesting proteins for MS/MS analysis is trypsin. PEAKS comes with an AAs/PTMs set, predefined for unmodified tryptic digests, to handle this common case. Tryptic peptides typically show excellent MS/MS spectra, and produce good sequences. If you wish to use a different enzyme, or sequence small peptides in entirety, you can create a new AAs/PTMs set and select another enzyme. Selecting an unknown enzyme places no restrictions on the residues appearing at the C-terminal end. You may set them yourself.
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