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Preparing MSFragger

Fengchao edited this page Jun 20, 2024 · 20 revisions

Downloading MSFragger (Academic License)

MSFragger is freely available for academic research, non-commercial or educational purposes. It can be downloaded directly from FragPipe GUI or from

Obtaining MSFragger (Commercial License)

For any uses other than academic research, non-commercial or educational purposes, Commercial Use License is required beyond the 60-day evaluation period.

  1. Complete the license agreement form to obtain 60-day evaluation license.
  2. Download MSFragger as described above.

For the commercial licensing details (e.g. pricing), please contact Drew Bennett ( Please contact Alexey Nesvizhskii at nesvi at if you have any other questions.

To read directly from Thermo (.raw) or Bruker (.d) spectral files, download the .zip version and unzip/decompress. Make sure the JAR (.jar extension) file is in the same directory as the 'ext' folder, which contains the libraries needed for reading raw files directly.

**Please make sure Adoptium Java 11 Runtime Environment is installed.