Welcome to EasyProt's website!

EasyProt is a complete graphical and user-friendly software platform for the analysis of MS/MS data.
For a more comprehensive description of EasyProt and EasyProtConv, feel free to read EasyProt - An easy-to-use graphical platform for proteomics data analysis, which was published in Journal of Proteomics in December 2012. Additionally, we would be grateful if you were to cite the above article in the event you used EasyProt in your research.

EasyProt is divided into two distinct parts:

EasyProt is now available as a virtual machine, so no installation is required and it can run on any system! Check the download section for more information.
EasyProt and EasyProtConv are freely available and can be both downloaded from the download section of the site.
We strongly recommend you to check the download page on a regular basis as both EasyProt and EasyProtConv are updated pretty frequently!
A description of the changes, including the whole history is available in the change log.

Frequent updates

The EasyProt platform is updated on a regular basis. You can see the latest changes by looking at the development transaction log here.


EasyProt is a java web application providing everything one needs to perform protein identification, protein quantification and export of results in popular data formats.

EasyProt's Key Features:
  • User friendly graphical interface
  • Multi-user web application
  • Protein identification through Olav (i.e. Phenyx) algorithm
  • On-the-fly dynamic FDR computation
  • Isobaric protein quantification
  • Label-free protein quantification
  • Stable isotope quantification (eg. glycations)
  • Unexpected PTM search through Popitam
  • Multiple data viewers (protein coverage, spectrum viewer, FDR viewer, etc.)
  • Multiple data exports (Excel, pep/protXML, PRIDE, etc.)


EasyProtConv is a standalone graphical desktop java application used to create peak lists as well as label-free maps required by EasyProt when performing label-free quantitation.

EasyProtConv's Key Features:
  • User friendly graphical interface
  • Generation of MGF files from Thermo RAW files or mzXML files
  • Isotopic correction
  • Charge deconvolution
  • MS3 data extraction
  • Label-free pre-processing: MS1 peak extraction and alignment of multiple runs
  • MS2/MS3 peak filtering
  • HCD/CID spectra merge
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