Launching MSFragger

Ensure that you have placed MSFragger.jar in your working directory and have modified the parameters file to reference your protein database. MSFragger generates auxiliary files during database search so it is critical that MSFragger must have write access to the directories containing the protein database AND the MS/MS data files.

Determine the amount of system memory available that you would like to make available to MSFragger. This will be specified by the Java maximum heap size parameter -Xmx (e.g. -Xmx3700M for 3700 MB or -Xmx8G for 8GB).

MSFragger takes the first argument as the input parameters file, followed by a list of one or more MS/MS data files.

Examples:

java -Xmx8G -jar MSFragger.jar fragger.params HeLa_run1.mzML HeLa_run2.mzML
java -Xmx8G -jar MSFragger.jar fragger.params *.mzML

The -Xmx flag is very important to ensure that MSFragger has access to sufficient memory to efficiently perform the search as the default max heap setting in Java is ¼ of total system memory (which is insufficient for optimal performance). We recommend that you can allocate a minimum of 4G or 6G for standard tryptic digestions.