Preparing MSFragger

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, selecting "60-day Evaluation Use License" option.
2. Download MSFragger as described above.

Please contact Alexey Nesvizhskii at nesvi at med.umich.edu if you have any 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 Oracle Java 8 Runtime Environment is installed.