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Preparing MSFragger

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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 http://msfragger-upgrader.nesvilab.org/upgrader/.

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 the license.
  2. Download MSFragger as described above.

For the commercial licensing details (e.g. pricing), please contact Drew Bennett (andbenne@umich.edu). Please contact Alexey Nesvizhskii at nesvi at med.umich.edu 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.

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