Preparing MSFragger

Obtaining MSFragger (Academic License)

MSFragger is freely available for academic research, non-commercial or educational purposes. If you have not downloaded MSFragger before, please complete steps 1-3. To upgrade to the most recent version from a previously downloaded version (JAR file), skip to step 3.

1. Complete the license agreement form on the University of Michigan Office of Tech Transfer website, selecting Academic and Research Education Use License.
2. Download MSFragger software using instructions received by email.
3. Update to the latest version of MSFragger (if you still qualify for Academic License, ) from the upgrade site.

Obtaining MSFragger (Commercial License)

For any uses other than academic research, non-commercial or educational purposes, Commercial Use License is required.

1.  Please Complete the [license agreement form](https://umich.flintbox.com/?embed=true#technologies/a8dd00a2-c057-4125-823b-adffac748490), selecting 60-day Evaluation Use License.
   

2. Download MSFragger software using instructions received by email.
3. Contact Alexey Nesvizhskii at nesvi at med.umich.edu to obtain the latest version of MSFragger.

4.  Purchase the commercial license through the Office of Tech Transfer if you would like to continue using MSFragger beyond the 60-day evaluation period.   
   

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.