running comet on linux (fedora)

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Florian Prodinger

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Feb 27, 2023, 9:42:19 PM2/27/23
to Comet ms/ms db search support
Hello everyone!

I wanted to ask how I can run comet on linux . I am using "Scientific Linux 7.9" which should be centos/fedora.
I have found an exe file (comet.linux.exe) in the download section of the comet homepage, but I have never run exe files on linux. To be honest, I thought it is not possible to use exe extension files on linux. I should also mention, I am not root and I do not have super user access.

If the comet.linux.exe file is the correct file for linux, is the inteded way of running comet on linux really using 3rd party software like Wine?

I looked around a little bit but could not find any documentation specifically for running comet on linux. I hope my question has not been asked before and is not in the docs, if this has been asked before kindly link me to the discussion.

Thank you very much for reading and I am looking forward to your reply.
Florian

David Tabb

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Feb 28, 2023, 2:03:25 AM2/28/23
to Comet ms/ms db search support
Hi, Florian.  Welcome to the fine world of Linux bioinformatics!

Linux does not care what the file suffixes are, unlike Windows.  In this case, I believe Jimmy is simply using ".exe" to indicate to users which files are binaries.  What Linux will care about is whether or not the file has an executable bit set (as in chmod +x comet.linux.exe).  It should be possible to run this from your own directory rather than /usr/bin, even without sudo permissions.  I do not believe that the Linux build requires .NET libraries, so I think you will not need Mono, let alone Wine.

Good luck!

Thanks,
Dave

Jimmy Eng

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Feb 28, 2023, 2:45:40 AM2/28/23
to Comet ms/ms db search support
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

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Jimmy Eng

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Mar 1, 2023, 2:52:42 PM3/1/23
to Comet ms/ms db search support
Florian,

I'm not sure why but your replies to this conversion (that you have since deleted presumably since they did not show up) were in "pending" state that required approval to be posted.  I'm not sure why that was the case as the group settings allow any member of this group to post.  Anyways, hopefully you're on the right path and good luck with your analysis.

Jimmy

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