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. > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
