Peptide Sequence Analysis

In mass spectrometry (MS)–based protein studies, peptide fragmentation analysis (i.e., MS/MS experiments such as matrix‐assisted laser desorption ionization [MALDI]–post‐source decay [PSD] analysis, collision‐induced dissociation [CID] of electrospray‐ and MALDI‐generated ions, and electron‐capture and electron‐transfer dissociation analysis of multiply charged ions) provide sequence information and, thus, can be used for (i) de novo sequencing, (ii) protein identification, and (iii) posttranslational or other covalent modification site assignments. This chapter offers a qualitative overview on which kind of peptide fragments are formed under different MS/MS conditions. High‐quality PSD and CID spectra provide illustrations of de novo sequencing and protein identification. The MS/MS behavior of some common posttranslational modifications such as acetylation, trimethylation, phosphorylation, sulfation, and O‐glycosylation is also discussed.