Creating CHIMERYS Workflows - Proteome Discoverer Software - Creating CHIMERYS Workflows - Proteome Discoverer Software - Proteome Discoverer Software

The CHIMERYS node receives MS/MS spectra from the Spectrum Selector, uploads the spectra and the user-selected FASTA file to the CHIMERYS service on the cloud, and receives the Mokapot output file from the CHIMERYS analysis. Alternatively, the CHIMERYS node can be instructed to receive the results from the CHIMERYS search prior to Mokapot and runs Mokapot on the local Proteome Disocverer client PC. CHIMERYS identifies substantially more PSMs for complex proteomics datasets than other search engines available in Proteome Discoverer, including Sequest HT. CHIMERYS supports the same types of peptides that are supported by INFERYS Rescoring, including the PTMs carbamidomethyl-cysteine, TMT/TMTpro-labeled lysine and N-terminus, and oxidized methionine, CID and HCD MS/MS, and peptide precurors from 1-6+.

To include CHIMERYS in a workflow, it is best to start with one of the default templates. There are templates that include CHIMERYS that perform label-free quantification and reporter ion quantification using TMT and TMTpro:

PW_Astral_CHIMERYS_DIA.pdProcessingWF

PW_Astral_CHIMERYS_DIA_MBR.pdProcessingWF

PWF_Hybrid_DIA_CHIMERYS.pdProcessingWF

PWF_Hybrid_DIA_CHIMERYS_MBR.pdProcessingWF

PWF_Hybrid_TMT_MS2_CHIMERYS.pdProcessingWF

PWF_Hybrid_LFQ_CHIMERYS.pdProcessingWF

PWF_Tribrid_LFQ_CHIMERYS_ITHCD_CID.pdProcessingWF

PWF_Tribrid_LFQ_CHIMERYS_OTHCD.pdProcessingWF

The workflow above that supports ion trap CID and HCD MS/MS data includes a “Top N Peaks Filter” node prior to the CHIMERYS search node. This filter significantly improves results for CHIMERYS searches for ion trap MS/MS data. Thermo Fisher Scientific recommends using the CHIMERYS node for this type of analyses.

Special Consensus Workflow Nodes and Node Settings

Choose the consensus workflow depending on the type of quantification methods that were used in the Processing workflow. If no quantification is performed, any of the CWF_Basic or the CWF_Comprehensive_Enhanced_Annotation workflows are suitable. If quantification nodes were added to the workflows, choose the appropriate consensus workflow for that quantification method. A description of these workflows in the sections immediately preceding this one.

CWF_Comprehensive_Enhanced Annotation_DIA.pdConsenusWF