The newest release of Thermo Scientific Proteome Discoverer 2.5 software provides higher confidence peptide identification, more accurate quantification and higher throughput data analysis than previous versions. The intelligent software uses deep learning facilitated by a Prosit-derived neural network, licensed in collaboration with MSAID GmbH, to provide more accurate prediction of fragmentation mass spectra. The technology enables more confident results in applications such as human leukocyte antigen (HLA) or metaproteomic analysis, which require large search spaces. Additionally, the new release includes a new enrichment service that helps provide biological meaning for differential analyses and support of targeted workflows. The software features tools to help deploy Thermo Scientific SureQuant Targeted Mass Spectrometry Assay Kits and custom SureQuant IS-triggered acquisition assays in new proteomics laboratories.