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 -~----------~----~----~----~------~----~------~--~---
