Sequence analysis of antimicrobial peptides by tandem mass spectrometry.

The emergence of new diseases as well as the increasing resistance of bacteria against antibiotics over the past decades has become a growing threat for humans. This has driven a sustained search for new agents that possess antibacterial activities against bacteria being resistant against conventional antibiotics and prompted an interest in short to medium-sized peptides called antimicrobial peptides (AMPs). Such peptides were isolated from different species, including mammals, insects, birds, fish, and plants. As these peptides circulate only at low concentrations in body fluids, a multidimensional purification strategy is obligatory to obtain pure peptides. The resulting low peptide amounts require highly sensitive analytical techniques to sequence the peptides, such as Edman degradation or mass spectrometry. Here we describe the protocols used routinely in our laboratory to identify peptides with antimicrobial activities by mass spectrometry including de novo sequence analysis.