Hi, Have you found a way to get the outfiles? I am trying to use the prot.XML output on TPP but in doesn t work. I also tried to run Sequest the command line, but it is not accepting the enzyme_number for trypsin. It is complaing about the enzyme description lines
*** Unknown sequest.params entry: 0. No_Enzyme 0 - - *** Unknown sequest.params entry: 1. Trypsin 1 KR P *** Unknown sequest.params entry: 2. Trypsin(KRLNH) 1 KRLNH - Thanks, 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 -~----------~----~----~----~------~----~------~--~---
