Expert search and TPP usage
From SPCTools
Eric's advice on November 11, 2008:
X! Tandem-K:
- To process 1 or more mzXML files, do this:
setenv SEARCHDIR XTK_HsIPI3.50_TargetDecoy
mkdir $SEARCHDIR
foreach file ( *.mzXML )
ln -s ../$file $SEARCHDIR/$file
end
cd $SEARCHDIR
cp /regis/sbeams/bin/tandem/tandem.params-cam tandem.params
vi tandem.params
echo “-ON” > xinteract.params
setenv TESTDEVPATH /tools/bin/TPP/tpp-dshteynb/bin
/sbeams/bin/tandem/runtandemsearch *.mzXML
(TPP is automatically run on the search results based on whatever is in xinteract.params and whole log emailed to you)
If you want to rerun the TPP on a dataset, do:
/bin/rm interact*
/bin/rm zztandem*
setenv TESTDEVPATH /tools/bin/TPP/tpp-dshteynb/bin
/sbeams/bin/tandem/finishtandemsearch --nowait *.mzXML >& zztandempostprocessing.log
(the --nowait is required so that the finisher doesn’t want around for the .done files)
Note that runtandemsearch and finishtandemsearch will also run on *.mgf or *.mzData or *.pkl
SpectraST:
- To process 1 or more mzXML files, do this:
setenv SEARCHDIR SST_HsNISTIT2.0_aDECOY1
mkdir $SEARCHDIR
foreach file ( *.mzXML )
ln -s ../$file $SEARCHDIR/$file
end
cd $SEARCHDIR
cp /regis/sbeams/bin/spectrast.params .
vi spectrast.params
echo “-OPd -dDECOY” > xinteract.params
setenv TESTDEVPATH /tools/bin/TPP/tpp-dshteynb/bin
/sbeams/bin/spectrast/runspectrast *.mzXML
(TPP is automatically run on the search results based on whatever is in xinteract.params and whole log emailed to you)
If you want to rerun the TPP on a dataset, do:
/bin/rm interact*
/bin/rm zzpost*
setenv TESTDEVPATH /tools/bin/TPP/tpp-dshteynb/bin
/sbeams/bin/spectrast/finishspectrastsearch --nowait *.mzXML >& zzpostprocessing.log
(the --nowait is required so that the finisher doesn’t want around for the .done files)
Notes:
- I do recommend the using a cutting-edge TESTDEVPATH:
setenv TESTDEVPATH /tools/bin/TPP/tpp-dshteynb/bin
but keep in mind that this is DEV. Not everyone may like this. It uses iProphet automatically. If you don’t specify TESTDEVPATH, iProphet is not currently run. Maybe it should be.
- For Xtandem, let’s not use the semi-parametric model.
- For SpectraST, let’s DO use the semi-parametric model.
- iProphet and MHT confidence scores are good. Let’s use them. Confidence scores are conservative but good.
- I think LOGPROBS is a bust. I’m not recommending them at the moment.
