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The Intelligent Search Algorithm for Proteomics

CHIMERYS 2.0: Unifying the analysis of DDA, WWA, DIA, AND PRM data
Integrated into Thermo Scientific™ Proteome Discoverer™ 3.1 software

  • Data-Independent Acquisition (DIA)

  • Parallel reaction monitoring (PRM)

  • Compatible with phosphorylated Ser, Thr, and Tyr residues

  • Enhanced parallelization and improved runtime

Explore our extensive FAQ Guide

Unleash the hidden potential of CHIMERYS with our comprehensive FAQs page. Delve into a wealth of information about the software's wide range of features, helpful usage tips, seamless compatibility, and effective troubleshooting solutions.

Unifying software for DDA, DIA and PRM data

  • One unifying, spectrum-centric and library-free approach for the analysis of peptide tandem mass spectra irrespective of acquisition type

  • Consistent false discovery rate estimation and post-processing, facilitating fair comparisons of DDA and DIA data

  • Label-free quantification at MS1 or MS2 level, as well as TMT™- and TMTpro™-based quantification

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Now supporting phosphopeptide predictions

  • Prediction of fragment ion intensities and retention times for unmodified and phosphorylated peptides, as well as peptides with methionine oxidation

  • Explain more experimental intensity and extend phosphoproteome coverage with the help of predictions for common neutral losses

  • Improved localization accuracy for INFERYS Rescoring and CHIMERYS based on fragment ion intensity predictions

Enhanced User Experience

  • Introducing Mokapot: accelerated false discovery rate estimation for peptide spectrum matches enabling big data proteomics

  • Increased computational efficiency and parallelism: accelerating time to insight for more data on the same subscription plan

  • Improved sensitivity and identification rates to dig even deeper into newly acquired and previously analyzed data

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"We have been highly impressed with CHIMERYS, which allows us to now quantify >3,000 proteins from single cells. We simply widen our isolation window in a DDA workflow and let CHIMERYS do the work of confidently assigning fragment ions to multiple peptides in each MS2 spectrum.”


Ryan Kelly, PhD
BYU Department of Chemistry and Biochemistry, Provo, Utah, USA

"We are using the groundbreaking search algorithm CHIMERYS in our cutting edge single-cell proteomics platform to accurately and sensitively identify large number of peptides and proteins from our samples. CHIMERYS excites us by surpassing conventional search engines by a factor of 2.6 in terms of ID rate.”

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Karl Mechtler
Vienna BioCenter, Vienna, Austria

Experience CHIMERYS in Proteome Discoverer Software

INFERYS and CHIMERYS are integrated into Proteome Discoverer software. For more information and licensing, please visit If you would like to learn about our data analysis services, feel free to contact us!

Thermo Scientific™ Proteome Discoverer™ software, Thermo Scientific™ Orbitrap™, and Thermo Scientific™ Q Exactive™ are trademarks of Thermo Fisher Scientific, Inc. Tandem Mass Tag, TMT™, and TMTpro™ are trademarks of Proteome Sciences plc. SEQUEST is a trademark of the University of Washington.