Orbitrap Illustration


Thermo Scientific™ ProSightPC software is the first stand-alone software for analyzing top-down and middle-down proteomics data, including the characterization of proteins with known PTMs.


  • Protein sequence identification
  • Protein and proteoform identification
  • Error tolerant identification of modifications, truncations, etc


  • Searching power of ProSightPC in the shell of Proteome Discoverer


  • Peptide sequence identification
  • Protein and proteoform identification

Software Overview for ProSightPC

Rapidly identify and characterize proteins, peptides, and PTMs, using the multiple search modes provided by Thermo Scientific™ ProSightPC software. ProSightPC software accommodates data generated by multiple fragmentation techniques and processes all accurate-mass MS/MS data, from top-down and middle-down experiments. It is the only proteomics software that allows the user to search MS/MS data against proteome warehouses containing the biological complexity present in UniProt. Specifically, the application does the following:

  • Supports top-down and middle-down experiments. Includes five different search modes-Accurate Mass, Biomarker, Sequence Tag, Single Protein, and Gene Restricted search to determine exact protein sequence including modifications and alternative splicing

  • Processes fragmentation data generated by HCD, ETD, EThcD, ECD, IRMPD or CID

  • Includes the proprietary ProSight Warehouse containing all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs)

  • Imports FASTA databases and shotgun annotates them with all possible modifications

  • Includes Sequence Gazer, which allows users to review search results and add, remove, or change modifications to find better fits

Featured Literature

Optimizing Top Down Analysis of Proteins on Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer
Seema Sharma, Parag Mallick, Tanya Stoyanova, Christopher Mullen, Chad Weisbrod, Jesse Canterbury, David Horn, Vlad Zabrouskov
Poster Note

The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics
LeDuc RD1, Fellers RT, Early BP, Greer JB, Thomas PM, Kelleher NL.
J Proteome Res. 2014 Jul 3;13(7):3231-40

Optimization of LC/MS Intact /Top-Down Protein Analysis on an Orbitrap Fusion Mass Spectrometer
Rosa Viner; Seema Sharma; Jesse D. Canterbury; David M.Horn; Vlad Zabrouskov