For an orbi/ltq run, myrimatch.cfg might look like: PrecursorMzTolerance = 10 PrecursorMzToleranceUnits = ppm FragmentMzTolerance = 0.5 FragmentMzToleranceUnits = daltons ProteinDatabase = c:\foo\bar.fasta NumMinTerminiCleavages = 1 CleavageRules = trypsin/p DynamicMods = M * 15.9949 C * 57.0215 UseChargeStateFromMS = true UseAvgMassOfSequences = false
Also, you might try BumberDash which is our fairly new GUI wrapper for the Bumbershoot tools. It includes a configuration editor.
http://fenchurch.mc.vanderbilt.edu:37280/repository/download/bt50/744:id/BumberDashInstall.msi?guest=1 Hope this helps, -Matt On 11/23/2010 5:34 PM, Chris Rath wrote:
Hi: I have heard good things about Myrimatch and would like to compare it with results from my usual Tandem, Mascot, and OMSSA processing in the TPP. The only problem is that I while I can run the program from the command line, I am having trouble searching with anything but the default options. The documentation (http://fenchurch.mc.vanderbilt.edu/bumbershoot/ myrimatch/index.html) suggests using a .cfg file "myrimatch.cfg" however I cannot get this to work. Does anyone have a sample .cfg file that I can use as a template? Thanks, -Chris
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