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 for quantitation. It supports multiple database search algorithms (SEQUEST, Z-Core, Mascot, etc.) and multiple dissociation techniques (CID, HCD, ETD) for more comprehensive analyses.

Product Description

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, Z-Core, Mascot, etc.) 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) and heavy-peptide techniques, enabling relative or absolute quantitation
  • Leverages high-mass-accuracy MALDI data in a Mascot-based peptide mass fingerprinting workflow
  • Validates protein IDs with false discovery rate (FDR) determination

Productive and Expandable

  • Automates data analysis
  • Simplifies analysis of MSn data using wizards and customizable workflows
  • 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) 
  • Provides a seamless transition from Thermo Scientific™ BioWorks™ platform using the SRF file import wizard
  • Expands through the integration of custom software tools


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

Proteome Discoverer

Comp- rehensive proteomics data analysis

Comprehensive data analysis is essential to successful protein identification, characterization, and quantitation.  Proteome Discoverer software supports multiple dissociation techniques, quantitation technologies, and database search algorithms for greater confidence.

Improved coverage

Use of multiple fragmentation modes can increase proteome coverage, especially for PTMs.  Hybrid ion trap-Orbitrap mass spectrometers with optional ETD and Proteome Discoverer software make it possible.

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