Thermo Scientific Proteome Discoverer 3.0 software

Thermo Fisher Scientific and MSAID have collaborated to provide proteomics researchers with mass spectrometry software that is designed to generate biological insight from acquired data by increasing peptide identification and quantitation capabilities using artificial intelligence (AI) and deep learning. Thermo Scientific Proteome Discoverer 3.0 software combines with the CHIMERYS search engine by MSAID to help Thermo Scientific Orbitrap mass spectrometer users to interpret the data generated by their instruments, leveraging AI to enhance the identification rate and number of unique peptide identifications in proteomics data. AI enables deep mining of proteomics data.

Previous technologies have been unable to fully interpret data generated using mass spectrometry, as mass spectra can contain fragments from multiple co-isolated peptides that cannot be identified using current algorithms. 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 is said to provide 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 datasets when compared to existing tools. In addition to improved protein coverage and quantitation capabilities, the software and search engine also facilitate fast data acquisition for increased sample throughput.

The software release includes an updated INFERYS prediction model, extending support to tandem mass tagging (TMT) and collisionally induced dissociation (CID) as well as providing results for immunopeptidomics. It also features the Comet search engine and a SureQuant method exporter node.