New comet user

[Daniel Nebauer]

Hello, having a problem, comet simply won't launch, I downloaded the latest release and when I attempt to open the win64.exe the screen simply flickers. I can open the comet UI but can't initiate a search. I hope I am missing something simple.

Thanks

[Jimmy Eng]

Hi Daniel.  If you're new to Comet, you probably don't want to attempt to binaries I release as they are just command line binaries to the search engine itself.  If you're clicking on the win64.exe binary, what's happening is that it is showing you the usage statement in a command prompt that then immediately disappears.  Because Comet itself isn't typically useful to most users without downstream visualization and post-analysis tools, your best bet is to use Comet within a software package like those listed on this page under "Comet integration" (e.g. TPP, PatternLab, Philosopher, SearchGUI, etc.).  I also don't recommend CometUI as it's too simplistic to be of real practical use.  But if you really would like to figure out why you can't run a search within CometUI, follow-up with me offline.  The most basic steps are:

• launch CometUI
• in the Tools menu select "Run Search"
• choose a fasta database and add a mass spec file (mzML, mzXML, Thermo RAW)
• hit the "run" button

That should be it.  There are Search Settings with a million options but those can be ignored until you're actually successfully able to run a search.  

Jimmy