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To get Compid, go to the Downloads section.

Starting Compid

Compid doesn't work by clicking compid.jar file, because the default memory heap settings are usually too small. Please use the startup scripts provided.


Compid requires Java runtime (JRE) version 6 or newer.

Importing Mascot DAT files

Compid supports using the freely available Mascot Parser plugin from Matrix Science to import DAT files created by Mascot. To enable this functionality, obtain the correct Mascot Parser version for your platform from Matrix Science.

Unarchive the file and place the two files in java subdirectory to Compid's lib subdirectory from where Compid will implicitly find and utilize them. An alternative placement is ".compid" directory in your home folder. The files are named msparser.jar and [msparserj.dll (for Windows) or (for Linux)]. It is imperative to get both files from the same archive.

Concerning Memory

Compid uses quite a lot of memory for some operations.

If memory runs out (you see OutOfHeapSpace exceptions), edit the startup script file (compid.cmd or and increase the -Xmx parameter. A good idea would be to do it in 50 MiB increments.

If you use Mascot Parser plugin and it crashes the software with ACCESS_VIOLATION errors, it is usually because too much memory is allocated. To fix this, lower the -Xmx and -Xms parameters in startup scripts.

Default values for -Xms and -Xmx Java parameters, which seem to work well for most computers with at least 1 GiB of memory are: -Xms128m -Xmx850m

Remember to start Compid with the script in question and not by running compid.jar.


Compid itself is licensed with GNU General Public License 3 (or later). For information on licenses of other software included in Compid, see NOTICE file.


Compid: A New Software Tool To Integrate and Compare MS/MS Based Protein Identification Results from Mascot and Paragon: J. Proteome Res., 2010, 9 (12), pp 6795–6800. The article is available here.