Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzer

Abstract Parallel collision‐induced dissociation (CID) of peptides rather than serial, as is customary, results in loss of the obvious parent‐fragment ion lineage available from CID on a single ion. We report proof‐of‐principle results suggesting the feasibility of parallel peptide CID, referred to here as shotgun CID, for protein identification when using the measured mass accuracies available from a time of flight mass analyzer and currently available search routines such as SEQUEST. Additionally, we report that parent‐fragment ion lineage may be reconstructed from information encoded in the chromatographic single ion current traces of peptides.