Proteome Discoverer Software

Comprehensive, expandable platform

Proteomics research requires more than just simple identification. Simplify the identification and quantification of proteins in complex biological samples for a wide range of proteomic workflows, from protein and peptide identification to PTM analysis to isobaric mass tagging and both SILAC and label-free quantitation.

Thermo Scientific Proteome Discoverer software offers a full suite of analysis tools with the flexibility to address multiple research workflows, and an easy-to-use, wizard·driven interface. Supporting multiple database search algorithms (SEQUEST HT, Mascot, Byonic, MS Amanda, and ProSightPD) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) delivering more comprehensive and complete analyses.

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Key benefits

Customize your data analysis for maximum coverage Perform relative quantitation Access workflow tools

Use the node-based workflow editor to customize your data analysis. Integrate database search results from multiple search engines such as SEQUEST, Mascot, MSAmanda, Byonic, and Thermo Scientific ProSightPD.

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

  • TMT SPS MS1
  • Glycopeptide identification and quantification
  • Phosphopeptide ID and quantification
  • Top-down proteomics
  • Cross-linking

Confidently interpret your data with sophisticated statistical and visualization tools unique to the Proteome Discoverer software.

Utilize multiple third-party algorithms, which are also integrated with our visualization and statistical tools to take your analysis to the next level.


Learn more

With support for multiple dissociation techniques, quantitation technologies, and database search algorithms enabling comprehensive protein identification, characterization, and quantitation, Proteome Discoverer is the comprehensive tool for your proteomic studies.

With a wide range of search algorithms from SEQUEST: Mascot, MS Amanda, Byonic and ProsightPD, the ability to combine the output from multiple algorithms allows cross-validation of results, increasing confidence in your decision making.

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

Additionally, full support for isobaric mass tagging with TMT and iTRAQ, as well as isotopic labelling with SILAC and label-free quantitation techniques provides complete experimental flexibility for your laboratory.

An example of a customizable workflow with eight separate searches on the same raw file.
Automate data analysis and simplify MSn data analysis through customizable workflows. An example of a customizable workflow with eight separate searches on the same raw file.
Proteome Discoverer 2.2 Tools for statistical and biological interpretation.
Proteome Discoverer Tools for statistical and biological interpretation. Includes study management for mapping of quantitation channels to biological information about the sample, with fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies.
Nodes that encapsulate 3rd party algorithms available in Proteome Discoverer.
Third party nodes for data processing, facilitates the processing of large datasets. Additionally, biological context by automatically annotating identified proteins with GO classifications, PTMs sites, and literature references from public databases (active maintenance required) can be illustrated.

Effective location of low-level sample components using creative data interrogation strategies such as generating inclusion and exclusion lists and importing those lists directly into instrument methods is provided, and data comparison, exchange, and verification with support for data standards developed by the HUPO Proteomics Standards Initiative (PSI) is additionally supported.

KEGG licence key access

If you are an existing customer, there is a new KEGG licence key which is valid for 2019.

To activate the KEGG license, navigate to Administration > Manage Licenses, click “Add Activation Code” and type in this license key:

WUC2-1MNB-D2GX-1MZ4

If you require assistance, please contact us for support ›


Featured content

Application note

Optimized Search Strategy to Maximize PTM Characterization and Protein Coverage in Proteome Discoverer Software

Application note

A Highly Sensitive and Robust 150 µm Column to Enable High-Throughput Proteomics

Application note

TMT Workflow on the Q Exactive Series - Instrument Parameter Optimization and Data Analysis in Proteome Discoverer 2.1 Software

Ordering guide