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Preparing MSFragger

Sarah Haynes edited this page Jul 31, 2019 · 2 revisions

Preparing Input Files

If running in the command line or through the Proteome Discoverer node, Thermo .raw files can be read directly. For all other raw file formats and FragPipe, MS/MS files need to be converted to mzML. See this tutorial on using ProteoWizard's msconvert tool.

Downloading MSFragger

If you haven't 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. Make sure Oracle Java 8 Runtime Environment is installed (

  1. Complete the license agreement form.
  2. Download the initial release of MSFragger software using instructions received by email.
  3. Once you obtained the MSFragger software, the latest version of the software can be downloaded (under the same license terms as the original version) using the Upgrade site. To read directly from Thermo raw files (when using MSFragger through PD or the standalone executable), download and unzip/decompress the .zip version of MSFragger. 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.
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