David, I am not using the Petunia interface, but command-line commands,and have just used a different naming convention. This has not been an issue with other files we have run in the past.
The process is this: (1)A 4GByte Agilent Data Directory (.d) was converted to a mzXML file via msconvert. (2)This mzXML file was converted to mgf using mzXML2Search. (3)The mgf file was submitted to Mascot for searching. (4) The resulting .dat file was submitted to Mascot2XML to create a peptideXML file (this process uses the mzXML file) (5)This peptideXML file was submitted to peptide Prophet using the xinteract command. There were several cascading issues in this process. -mzXML2Search produced a very small file compared with the what might be produced if msconvert --mgf option was used. I am still investigating why this is happening. -The Mascot result file yielded very few proteins (~20) with very low scores -The pepXML file has only a small number of entries (~10) -xinteract produced this error. Thanks for any suggestions you might have regards Simon On Jun 10, 1:46 am, David Shteynberg <[email protected]> wrote: > Hi Simon, > > This error indicates that the PepXMLViewer failed when it tried to > index your pepxml file. .pepprophet.xml is not a normal extension > produced by the TPP for a pepXML file. Can you describe exactly how > you arrived at this pepXML file? > > Thanks, > -David > > On Wed, Jun 9, 2010 at 1:46 AM, Simon Michnowicz > > > > <[email protected]> wrote: > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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.
