Hi Nikhil, I have put the files on this discussion group file upload:
http://groups.google.com/group/spctools-discuss/files?hl=en You will need to have Active Perl installed on you computer to use this script. http://www.activestate.com/activeperl/ To use the script runSequest.pl, you need to have both files (runSequest.pl and sequest.params) in the same folder of your rawfiles. The script will create a folder for each rawfile to put the .dta and .out files. You will need to edit the runSequest.pl to set the direction of DeconMSN.exe and sequest.exe on your system. On sequest.params, you will need to change the database direction according your experiment. Hope it helps. Regards, Daniel On Oct 18, 2:55 pm, Nikhil Garge <[email protected]> wrote: > Hello Daniel, > > Nice to know that you are able to address the issue of batch processing in > "Proteome Discoverer". I would really appreciate if you can forward the > script to me. I undserstand the part where you convert RAW files to DTA > files using DeconMSn. But then how do you perform SEQUEST search? > > Thanks, > ~Nikhil. > > On Sat, Oct 17, 2009 at 10:07 AM, Daniel Lorenzini <[email protected]>wrote: > > > > > > > Hi Nikhil, > > > I have found a solution for this batch processing problem with > > proteome discoverer. I wrote a perl script to run DeconMSn (PNNL) > > software to generate dta files from raw files and also run sequest to > > search my spectra against the db. The Proteome Discoverer doesn t come > > with a sequest.params file to run sequest on DOS, so I got one with > > Thermo tech support. Finally I use Unitemare (yates lab) to join > > the .out results into a .sqt file to analyse with DTASelect (yates > > lab). > > > Let me know if you want a copy of this script to run with your data. > > > Regards, > > > Daniel > > > On Sep 23, 4:44 pm, Nikhil Garge <[email protected]> wrote: > > > Hello, > > > > Anybody has experience using "Proteome Discoverer 1.0" software for > > SEQUEST > > > search. I use the Bioworks for SEQUEST search and new to "Proteome > > > Discoverer 1.0". few of my concerns are as follows: > > > > a) How to perform SEQUEST BATCH search using "Proteome Discoverer 1.0"? > > It > > > seems to accept only ine raw file at a time. Do you know how can one > > supply > > > multiple raw files for SEQEUST search? > > > b) The output is *.msf file which can be exported into protXML file > > format. > > > So does this mean "Proteome Discoverer 1.0" uses Protein Prophet > > algorithm > > > to identify significant proteins? > > > c) The SEQUEST search done through "Proteome Discoverer 1.0" doesnt seem > > to > > > output *.out files (or pepXML files). I am more interested in individual > > > peptide hits but dont see how one can get 1st and 2nd hit as we see in > > *.out > > > file using Bioworks). > > > > I would really appreciate your feedback on this. > > > > Thanks, > > > ~Nikhil.- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
