Thermo Scientific™

Proteome Discoverer™ Software

Identify and quantify proteins in complex biological samples using Thermo Scientific™ Proteome Discoverer™ software. Proteome Discoverer software simplifies a wide range of proteomics workflows, from protein and peptide identification to PTM analysis to isobaric mass tagging and both SILAC and label-free quantitation. It supports multiple database search algorithms (SEQUEST, Z-Core, Mascot, and Byonic) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) for more comprehensive analyses.

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Important note: Users with active maintenance licenses will be able to upgrade to Proteome Discoverer 2.4 software for no extra charge. However, the maintenance license has been discontinued starting with the Proteome Discoverer 2.4 software release. Instead, the annotation capabilities will be provided for all users of Proteome Discoverer 2.4 Base and Quan software without requiring the maintenance license. Maintenance licenses can still be used to upgrade from prior versions to Proteome Discoverer 2.4 software but will not be used to upgrade from version 2.4 to subsequence releases.

Proteome Discoverer software supports multiple dissociation techniques, quantitation technologies, and database search algorithms for comprehensive protein identification, characterization, and quantitation.


  • Provides a choice of search algorithms (SEQUEST: Mascot, MS Amanda, Byonic, ProsightPD) and can combine output from multiple algorithms to maximize and cross-validate results
  • Supports multiple dissociation techniques (CID, HCD, and ETD) for more complete coverage and confident identification of PTMs
  • Supports isobaric mass tagging (TMT, iTRAQ), isotopic labeling (SILAC), and label-free quantification techniques
  • Validates peptide and protein IDs with false discovery rate (FDR) determination

Productive and Expandable

  • Automates data analysis, and simplifies MSn data analysis through customizable workflows
  • Includes study management for mapping of quantitation channels to biological information about the sample
  • Provides 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
  • Illustrates biological context by automatically annotating identified proteins with GO classifications, PTMs sites, and literature references from public databases
  • Facilitates data comparison, exchange, and verification with support for data standards developed by the HUPO Proteomics Standards Initiative (PSI)
  • Supports third party nodes for data prcessing, and enables processing of large datasets and persistent reports
  • Fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies
  • Obtain reliable statistics and validate quantification results visually

Specifications, terms, and pricing are subject to change. Not all products are available in all countries. Please consult your local sales representative for details.