Get a full suite of customizable data analysis workflows for complex acquisition methods with Thermo Scientific Proteome Discoverer software. Gain the ability to manage datasets for statistical analyses, biological annotation, and data interpretation tools to simplify the identification and quantification of proteins in complex biological samples for a wide range of proteomics workflows. The software streamlines and enables multiple proteomics applications from protein and peptide identification to PTM analysis, isobaric mass tagging, and label-free quantitation. Proteome Discoverer software supports multiple database search algorithms and dissociation techniques to deliver more comprehensive and complete analyses.

Go beyond searching to discovering, with intelligent INFERYS™ Rescoring and the novel CHIMERYS™ intelligent search algorithm by MSAID. These innovative approaches substantially increase the identification rate and the number of unique peptide identifications. They also improve protein coverage and quantitation capabilities, facilitate more efficient data acquisition schemes, and enable scientists to generate more biological insights from their existing and newly acquired data.


Customize your data analysis Perform relative quantitationExtensible workflow tools

Use the node-based workflow editor to customize your data analysis for maximum coverage and confidence. Integrate database search results from multiple search engines such as SEQUEST™ HT, Mascot, MSAmanda, Byonic™ from Protein Metrics, and Thermo Scientific ProSightPD software. Increase confidence in peptide identification and quantification using INFERYS Rescoring and enable a deeper mining of data using the CHIMERYS intelligent search algorithm.

Measure and report the relative expression levels of isotopically labeled peptides for:

  • Glycopeptide identification and quantification
  • Phosphopeptide identification and quantification
  • Top-down proteomics
  • Cross-linking

Confidently and efficiently interpret your data with integrated statistical and visualization tools for a faster time to meaningful results.

Utilize third-party nodes and build in customization with the scripting node, while maintaining full integration into the Proteome Discoverer software framework to leverage visualization and statistical tools to take your analysis to the next level.

Comprehensive tools for proteomic studies

With a wide range of search algorithms and the ability to combine the output from multiple algorithms, Proteome Discoverer software increases confidence in results and decision making through cross-validation. Augment searches with intelligent INFERYS Rescoring to increase confidence in peptide identification and quantitation. Dig deeper into your data to uncover new insights using artificial intelligence with the CHIMERYS intelligent search algorithm to substantially increase the number of unique peptide identifications, improve protein coverage, and extend quantitation capabilities.

Complete sequence coverage and confident identification of post-translational modifications (PTMs) is realized with support for multiple dissociation techniques including collision induced dissociation (CID), higher-energy collision induced dissociation (HCD) and electron transfer dissociation (ETD) in tandem with built-for-purpose search engines.

Customizable data analysis workflows

Automate and simplify data analysis through customizable workflows including full support for multiple quantitative workflows. Enjoy experimental flexibility for quantitation by employing isobaric mass tagging with TMT or other isotopic labeling strategies or utilize label-free quantitation techniques. Map quantitative data to biological information through study management and leverage fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies.

Refine acquisition strategies by generating inclusion and exclusion lists that can be directly imported into instrument methods. Confidently and easily facilitate data comparison, exchange, and verification in compliance with data standards developed by the HUPO Proteomics Standards Initiative (PSI).

CHIMERYS Intelligent Search Algorithm How to Video

A how-to-video covering the basics of using the CHIMERYS intelligent search algorithm in the Proteome Discoverer software framework

KEGG license key access

If you would like to utilize KEGG pathways please visit  Pathway Solutions for a license.


Application notes

Additional resources


Style Sheet for Komodo Tabs
Style Sheet for Global Design System
Style Sheet for Global Design System
CMD SchemaApp code