• CHIMERYS™ 2.0: The CHIMERYS intelligent search algorithm has been improved to support data independent analysis and some types of parallel reaction monitoring analysis.
• INFERYS™ 3.0: The INFERYS prediction model has been updated to include the post-translational modification phosphorylation. The INFERYS prediction now also includes neutral loss fragments, including water, ammonia, carboxyl and phosphate losses.
• Mokapot: The CHIMERYS algorithm automatically uses the Mokapot algorithm for FDR control in place of Percolator. The Mokapot algorithm is 10 times faster and produces very similar results to Percolator. As a result, DDA analyses in CHIMERYS 2.0 are substantially faster than CHIMERYS 1.0 released in Proteome Discoverer 3.0.
• Fragment Ions Quantifier: This new node is used in the Consensus workflow to roll up DIA and PRM quantitative values from CHIMERYS to Peptide Groups and Protein levels. The parameters of the Fragment Ions Quantifier are the same as for the Precursor Ions Quantifier and Reporter Ions Quantifier nodes.
• Improved performance of the consensus workflow: The analysis time of the consensus workflow has been decreased by up about 20% with higher complexity datasets exhibiting a larger relative decrease in analysis time.
• Support for Orbitrap™ Astral™ mass spectrometer scan headers.
• New web browser-based Help portal for users with a network connection. For users without a network connection, a local Help file is available.