Proteome Discoverer™ Software

Employ a expandable platform for the analysis of qualitative and quantitative proteomics data with Thermo Scientific™ Proteome Discoverer™ Software.

Outstanding sensitivity and the rapid growth of public databases have made mass spectrometry the primary method of identifying proteins in complex biological samples. Proteome Discoverer was designed to address this need for flexibility by offering a wide array of bio-software tools and customizable workflows for every proteomics experiment.

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Product Description

Proteome Discoverer software is a comprehensive tool for proteomic data analysis. It supports multiple dissociation techniques, quantitation technologies, and database search algorithms for more confident and comprehensive protein identification and characterization. The Proteome Discoverer Daemon facilitates automated data analysis for greater productivity.

Key Features and Benefits

  • Multiple database search capability provides the option of applying multiple search algorithms (SEQUEST, Z-Core, Mascot, etc.) and combining their outputs to maximize and cross-validate results
  • Support for multiple dissociation techniques (CID, ETD, and HCD) and the ability to combine their results helps identify more PTMs and increase confidence in those identifications
  • Support for isobaric mass tagging (TMT, iTRAQ), and HeavyPeptide techniques enable relative or absolute quantitation
  • A Mascot-based peptide mass fingerprinting workflow leverages high-mass-accuracy MALDI data
  • False Discovery Rate (FDR) determination validates protein IDs
  • Wizards and customizable proteomics workflows simplify analysis of MSn data from raw spectra through protein annotation
  • Automated annotation of identified proteins with GO classifications, PTMs, and literature references from public databases illustrates biological context
  • Create data interrogation strategies such as generating inclusion and exclusion lists and import those lists directly into instrument methods enable more effective location of low-level sample components
  • Support for data standards developed by the HUPO Proteomics Standards Initiative (PSI) facilitates data comparison, exchange, and verification
  • SRF file import wizard provides a seamless transition from the Thermo Scientific BioWorks platform
  • Robust Proteome Discoverer software platform can be expanded through integration of custom software tools

Compatible with:

  • Xcalibur software
  • SIEVE software
  • ProSightPC software
  • PEAKS Studio software
  • ProMass Deconvolution software
  • LTQ family of linear ion trap mass spectrometers
  • LTQ Obritrap family of hybrid mass spectrometers
  • LTQ Ultra hybrid mass spectrometers
  • Electron Transfer Dissociation (ETD)
  • TSQ family of triple quadrupole mass spectrometers


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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Catalog #
Thermo Scientific Proteome Discoverer Software

Full specifications
For Use With LTQ Linear Ion Trap Mass Spectrometers; LTQ Obritrap Hybrid Mass Spectrometers; LTQ Ultra Hybrid Mass Spectrometers; Electron Transfer Dissociation; TSQ Triple Quadrupole Mass Spectrometers
Type Software
Description Thermo Scientific Proteome Discoverer Software

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