Abstract: Tandem mass spectrometry in a quadrupole ion trap is widely used for the characterization of peptide sequences. Sequence information is obtained from the fragments generated from the peptide ions after they have been energetically excited. The energized ions can decompose via random backbone cleavages, consecutive reactions, or selective cleavages, depending on sequence composition and charge type. The detailed fragmentation mechanisms of protonated and metalated peptides with one or more charges will be discussed and examples will be given on how to deduce the sequence of linear and cyclic peptides from the observed fragments. New sequencing strategies, involving dimetalated peptide ions, peptide anions, and peptide ions activated by electron transfer will also be presented.