For any mass spectrometry analysis, sensitive and reliable identification is key to maximising potential insights and discovery. interact-ms allows access to the inSPIRE rescoring pipeline for state-of-the-art identification in any experiment, and PEPSeek is a specialized tool for identification of pathogen peptides in infected immunopeptidome samples. In the latest release PISCES, a novel computational approach, eschews standard target-decoy methods and inherent biases, to provide an unbiased identification tool for noncanonical peptide identification. Further integrations can allow custom searches to be run with MSFragger, binding affinity via NetMHCpan, and quantification via Skyline to build out your analysis ecosystem entirely within interact-ms.