Alt NxST search strategy
From SPCTools
The instructions below are for searching MS/MS data from glycocapture experiments. It is based on a 2005 paper by Atwood and York http://www.peptideatlas.org/upload/Atwood-York_GlycopeptideSearchStrategy.pdf, but has been modified to work with the ISB version of Sequest.
- All work should generally be done as user sbeams
su sbeams
- set path to include scripts, bash syntax shown
export PATH=$PATH:/regis/sbeams/archive/sbeams/scripts
- create search database with NxS/T changed to NBS/T. This will
- make nxst and 'reverse' versions of the source database, called
- myfasta_nxst_db.fsa myfasta_reverse_db.fsa for the example shown.
make_nxst_db.pl myfasta.fsa
- Make search directory
mkdir HsIPI_v3.30plus_LTQ_nxst cd HsIPI_v3.30plus_LTQ_nxst
- Copy in template sequest.params file, which has static mass mod for B.
- Edit database to point at modified db
cp /regis/sbeams/archive/sbeams/conf/sequest.params.ft . mv sequest.params.ft sequest.params
- Add symlinks to mzXML files
ln -s /data2/search/yzhou/CP/LCQ/Prostate_*.mzXML .
- Run sequest
runsequest *.mzXML
- Generate xml from html results
ls *html | xargs batch_sequest_2_xml.sh
- Substitute search settings
ls *.pep.xml | xargs batch_convert.sh
- This step is still manual, substitute db name in pepXML files, as well as
- copy of sequest.params file
cp sequest.params sequest.params.run perl -pi -e 's/ipi.MOUSE.v3.24.fasta-mix7prot_nxst_db.fsa/ipi.MOUSE.v3.24.fasta-mix7prot.fsa/' *.xml sequest.params
- Create or copy over an appopriate xinteract command
cp /regis/sbeams/archive/sbeams/conf/xinteract.cmd.ft xinteract.cmd
- Run xinteract
./xinteract.cmd
- Run calctppstat.pl script to see results
calctppstat.pl --fu -g