Orbitrap Illustration


Thermo Scientific™ ProteinCenter software facilitates interpreting proteomics data – quickly extracting meaningful biological information from multiple, complex data sets. ProteinCenter is a web-based data interpretation tool keyed on unique protein sequences and annotations from the public domain.

Compare your datasets

  • Easy integration with Proteome Discoverer™ software
  • Import many data formats such as PRIDE.xml
  • Retain datasets and discoveries through time


Add biological meaning

  • Find the salient trends in your data
  • Search significant pathways and ontology terms

Include the latest information

  • Be assured that your protein annotations are current
  • Have many public annotation repositories monitored for you
  • Take advantage of frequent hands-free updates


Share your results

  • Cloud architecture permits immediate sharing with anyone, from any computer

Software Overview for ProteinCenter


ProteinCenter is a web-based tool that enables scientists to compare and interpret proteomics data sets in minutes and overcomes the hurdle of proteins existing under different names and accession keys in different databases.

ProteinCenter is regularly updated from all major protein databases, ProteinCenter provides a consolidated, biologically annotated, protein sequence database to enable filtering, clustering and statistical bioinformatic analysis from single, combined or comparison data sets.

ProteinCenter can reveal the biological context of each data set, in quantitative studies and for a single protein.


ProteinCenter Brochure

Reducing complexity and adding biological meaning to your data using knowledge bases
Slide Presentation

To get access to a trial version of ProteinCenter, e-mail proteincenter-support@thermofisher.com


Express Biological Pathway Analysis of Mass Spectrometry-Based P1189 Proteomics Datasets
Christian Ravnsborg, Martin Damsbo, Ole Vorm, Michaela Scigelova and Madalina Oppermann
Thermo Fisher Scientific

Systematic Integration Of “Omics” Data To Improve Innovation In Beer Crafting
Dunn B, Kvitek D, Carrera M, Jiang X, Tan G, Lopez-Ferrer D, Huhmer A.
ASMS 2015 Poster Note 64486