Comet and TPP with different reference proteomes.

Getting some odd results using the TPP for a .raw file of Rhonda’s. I think it’s an issue with the reference proteome used, so I want to test that here.

I fished Stevens file off his directory in Emu, and plan to use that raw file, and only change the proteome reference file to see if we get different results.

First, we need to run ReAdW to convert the .raw file to mzXML.

system("WINEPREFIX=~/.wine32 wine /home/shared/ReAdW/ReAdW.2016010.msfilereader.exe ~/Documents/ProtTest2/sample.raw ~/Documents/ProtTest2/sample.mzXML")

setwd("~/Documents/ProtTest2")

system("scp sample.mzXML sample2.mzXML")

system("comet.2016012.linux.exe -Pstevens.comet.params.high-low -DStevens.database.CgCont.fa sample.mzXML")

system("comet.2016012.linux.exe -Pstevens.comet.params.high-low -DSeans-gigas-proteome.fasta sample2.mzXML")

system("/usr/tpp_install/tpp/bin/xinteract -dDECOY_ -nsample2 sample2.pep.xml -p0.9 -OAp")

system("/usr/tpp_install/tpp/bin/xinteract -dDECOY_ -nsample sample.pep.xml -p0.9 -OAp")

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