Orbitrap Illustration

Proteome Discoverer



Thermo Scientific™ 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, and Byonic™) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) for more comprehensive analyses. Additionally, it supports third party nodes to handle data processing.

Peptide Identification

  • Peptide sequence identification
  • Protein identification


PTM analysis

  • Localization and identification of PTMs (glycosylation, phosphorylation, acetylation, etc.)
  • PTM quantification

Relative quantitation

  • Isobaric labeling based quantitation (TMT, iTRAQ)
  • Precursor ion quantitation (SILAC, dimethyl, O18)


Support of third party nodes

  • Byonic
  • Preview™
  • ProSightPC

Software Overview for Proteome Discoverer™


The Proteome Discoverer application is a client-server application that uses workflows to process and report mass spectrometry data. It compares the raw data taken from mass spectrometers or spectral libraries generated from mass spectrometers to the information from a selected FASTA database and identifies proteins from the mass spectra of digested fragments. You can use this application to analyze spectral data from all Thermo Scientific and other mass spectrometers.

Specifically, the application does the following:

  • Works with peak-finding search engines such as Sequest™ HT and Mascot to process all data types collected from low- and high-mass-accuracy mass spectrometers. The peak-finding algorithm searches the raw mass spectrometry data and generates a peak list and relative abundances. The peaks represent the fragments of peptides for a given mass and charge.
  • Produces complementary data from a variety of dissociation methods and data-dependent stages of tandem mass spectrometry.
  • Combines, filters, and annotates results from several database search engines and from multiple analysis iterations. The search engines correlate the uninterrupted tandem mass spectra of peptides with databases, such as FASTA.
  • Proteome Discoverer also supports isobaric mass tagging (TMT, iTRAQ) and heavy-peptide techniques, enabling relative or absolute quantitation.



Related Literature


Optimized Search Strategy to Maximize PTM Characterization and Protein Coverage in Proteome Discoverer Software
Jiang, X., Horn, D., Blank, M., Drew, D., Delanghe, B., Viner, R., Huhmer, A.
Application Note 658

TMT Workflow on the Q Exactive Series - Instrument Parameter Optimization and Data Analysis in Proteome Discoverer 2.1 Software
Jiang, X., Arrey, T., Damoc, E., Scigelova, M., Horn, D., Viner, R., Huhmer, A.
Application Note 649

New Method for Label-Free Quantification in the Proteome Discoverer Framework
Horn, D., Ueckert, T., Fritzemeier, K., Tham, K., Paschke, C., Berg, F., Pfaff, H., Jiang, X., Li, S., Lopez-Ferrer, D.
Scientific Poster

Evaluation of search engines for phosphopeptide identification and quantitation
Jiang, C., Horn, D., Bomgarden, R., Schroeder, T., Viner, R., Huhmer, A.
Scientific Poster