Proteome Discoverer Software

Comprehensive, expandable platform

Proteomics research requires more than just simple identification. 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.

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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.

Customized data analysis

An example of a customizable workflow with eight separate searches on the same raw file.
An example of a customizable workflow with eight separate searches on the same raw file.

Relative quantitation

Proteome Discoverer 2.2 Tools for statistical and biological interpretation.
Proteome Discoverer 2.2 Tools for statistical and biological interpretation.

Workflow tools

Nodes that encapsulate 3rd party algorithms available in Proteome Discoverer.
Nodes that encapsulate 3rd party algorithms available in Proteome Discoverer.

Customized data analysis

An example of a customizable workflow with eight separate searches on the same raw file.
An example of a customizable workflow with eight separate searches on the same raw file.

Relative quantitation

Proteome Discoverer 2.2 Tools for statistical and biological interpretation.
Proteome Discoverer 2.2 Tools for statistical and biological interpretation.

Workflow tools

Nodes that encapsulate 3rd party algorithms available in Proteome Discoverer.
Nodes that encapsulate 3rd party algorithms available in Proteome Discoverer.

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