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