Thermo Fisher Scientific and MSAID have collaborated to combine the Thermo Scientific Proteome Discoverer 3.0 software with CHIMERYS from MSAID. This uses artificial intelligence to enhance the identification rate and number of unique peptide identifications in proteomics data. CHIMERYS identifies a minimal set of peptides that can explain the acquired tandem mass spectrum, in comparison to existing methodologies, which typically assume all peaks in a tandem mass spectrum are derived from a single peptide. This approach provides a 1.8-fold increase in the number of unique peptide identifications and a 1.5-fold increase in the number of protein identifications for typical proteomics data sets when compared to existing tools. In addition to improved protein coverage and quantitation capabilities, Proteome Discoverer 3.0 software paired with CHIMERYS also facilitates faster data acquisition for increased sample throughput. The Proteome Discoverer 3.0 software release also includes an updated INFERYS prediction model, extending support to tandem mass tagging, collisionally induced dissociation and providing improved results for immunopeptidomics.