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. 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.