Understanding how the CHIMERYS algorithm quantifies data produced by Data Independent Acquisition - Proteome Discoverer Software - Understanding how the CHIMERYS algorithm quantifies data produced by Data Independent Acquisition - Proteome Discoverer Software - Proteome Discoverer Software

The CHIMERYS algorithm is built on INFERYS, a deep neural network predicting physicochemical peptide properties such as retention time and fragment ion intensities, and employs a novel spectrum deconvolution approach. This algorithm substantially increases the number of peptides that can be identified in complex proteomic datasets generated using data dependent acquisition (DDA) compared to traditional search engines, such as Sequest HT. For quantification, CHIMERYS can be paired with either the Reporter Ions Quantifier for TMT quantification or the Minora Feature Detector for MS1-based label-free quantification in Proteome Discoverer 3.0.

CHIMERYS now also supports the identification and label-free MS2-based quantification of peptides from data independent acquisition (DIA) and parallel reaction monitoring (PRM) data. For each identified peptide, CHIMERYS returns peak areas for each charge state. The list of available nodes in the Consensus workflow was extended with a new Fragment Ions Quantifier node, which produces quantitative values for Peptide Groups and Proteins.