Florian,
Everything that Dave has said is spot on. And I'm glad Dave responded because I did not get email notification of your original post but I did get notified of Dave's reply.
Here are some more verbose instructions for running a Linux search:
Grab the comet.linux.exe binary, make sure it is executable by running the "chmod" command that Dave stated ("chmod +x comet.linux.exe"). Then just execute the program by running "./comet.linux.exe" or "/whatever/the/full/path/is/comet.linux.exe". You should see a little Comet help screen with a few command line options.
Now to run a search, you will need:
- a "comet.params" file (which contains all of the search options that you can set)
- a protein sequence database
- some spectral data file, typically an mzML or mzXML file
One way to get a "comet.params" file is to download
one of the example files (for Comet 2023.01.0) at the top of this page: The files you want will be "comet.params.low-low", "comet.params.high-low", and/or "comet.params.high-high". Whichever one you download, rename it to simply "comet.params". Then edit this text file and set the "database_name" parameter entry value to a valid sequence database. If you have a sequence database as "/my/path/database/human.fasta" then the database entry should be specified as "database_name = /my/path/database/human.fasta". Go ahead and also set "output_txtfile = 1" to have Comet create a tab-delimited text output (in addition to the pepXML output). Unless you can consume pepXML files, the tab-delimited text output is easier to digest. The params file with ".low-low" extension is meant to be applied to low-res MS1 + low-res MS2 data. The file with the ".high-low" extension is meant to be applied to high-res MS1 + low-res MS2 data. And the file with the ".high-high" extension is meant to be applied to high-res MS1 + high-res MS2 data.
Once you have (a) the executable Comet binary, (b) a "comet.params" file with the sequence database set, and (c) a spectrum file (we'll use "somefile.mzML" as an example), you can run a search using the command "./comet.linux.exe somefile.mzML". After the search is completed, you will end up with two output files: "somefile.txt" and "somefile.pep.xml".
Comet just generates raw search results and nothing more. No FDR analysis. No protein inference. So you'll have to figure out what you want to do with the Comet output. If raw search results aren't what you're interested, there are a number of software suites with post-processing tools that incorporate Comet,
most of which are listed under the "Integration" section of this page.
I'll add a page to the "
Notes" section of Comet's website with this information tomorrow. Good luck running a Comet linux search and definitely follow-up here if anything isn't clear or if you run into any issues.
Jimmy