Hello everyone, I'd like to pile on with a few OMSSA questions. I'd like to include OMSSA, probID and Tandem in an automated search scheme for the same data and this is proving problematic when managing the OMSSA output. First a quick overview...
I run an OMSSA search from the command line on an MGF file converted from an mzXML using the -op and an e-value cutoff of 1e6 to get a pep.xml output with plenty of decoy hits from the database. When the search is complete I edit the resulting pep.xml file summary_base_name and search_base_name lines to point at the mzXML file rather than the output pep.xml. I then run interactparser with the-P option to fix the protein names, and refreshparser to point to the correct database. >From here I can succesfully take the file through each of the parser steps like found in some of the other threads in this group: i.e. interactparser out.pep.xml-L5 - Etrypsin -C -P fix.pep.xml refreshparser fix.pep.xml c:\blastdb\omssaTMP.fasta peptideprophetparser fix.pep.xml DECOY=decoy_ MINPROB=0 NONPARAM proteinprophet fix.pep.xml fix.prot.xml NOOCCAM NOGROUPS However trying to read the file with pep.xml viewer just gives me the error message: unable to read pepxml file: error parsing pepxml file: XML parsing error: not well-formed (invalid token), at xml file line 11, column 62 The Prot.xml is viewable. Running all steps through Xinteract also crashes at pepxmlviewer step. Has anyone been able to take their OMSSA results through the TPP in such a way that the final pep.xml is viewable with pepxmlviewer? If you have an example of a working pep.xml file or a quick workflow to share that would be excellent. On a side note all analysis of OMSSA pep.xml I have seen use MINPROB=0 for the peptideprophetparser step, is there a reason for this? Why don't I want to exclude lower probability peptides in OMSSAs case, and is Occams razor and protein grouping not applicable in OMSSAs case? Since I'd like to combine the OMSSA output with other output this is something that I'd like to understand before proceeding. If anyone has the time and energy to give me any input on this it would be much appreciated. /Erik -- 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.
