Dear Group, I ran xinteract on a pepXML file that was generated from a Mascot search, and it exited with an error message.
command "/mnt/sanfs/APCF-PROD/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi - I /mnt/sanfs/APCF-PROD/results/tpp/2010-06-08/simon- J2468.pepprophet.xml" exited with non-zero exit code: 11 I am afraid I do not know what this error means. I found the input pepXML only had a few number of entries, so am I right to think that this is cause of the error?(The Mascot search was done using incorrect parameters, resulting in a poor output) I have two questions: (1) How much data do you need to provide a satisfactory run for peptideProphet? Is it possible to check this before calling xinteract? (2) I looked at the .dat=>pepXML conversion via Mascot2XML. I expected a 1:1 mapping for proteins, however I found only a subset of proteins being placed in the file. Is there some internal filtering that occurs here? The scores were all low, which might have taxed any algorithm to do this. Much thanks for any assistance. Simon Michnowicz -- 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.
