Simon, I may have the answer to some of the issues...
msconvert will create mzXML files in which spectra are numbered using the Agilent native scan IDs. These are large and not consecutive. MzXML2Search was written assuming consecutive scan numbers starting from 1. By default the maximum scan number it outputs is 99999 due to a default value in the code (if I recall correctly). You need to run MzXML2Search with an arbitrarily large -L parameter (last scan) when giving it MzXML from msconvert. This should give you a full-length mgf file, and consequently more IDs as you'd expect. There is a thread about this somewhere in the archives of this group that Matt Chambers (proteowizard developer) contributed to. We stick to using trapper for Agilent conversions at the moment, as this numbers scans consecutively from 1. Cheers, DT > -----Original Message----- > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of Brian Pratt > Sent: 10 June 2010 16:44 > To: [email protected] > Subject: Re: [spctools-discuss] Re: xinteract question > > To your last point "xinteract produced this error", xinteract just > spins up other programs in turn, The crash you are seeing is indeed > in "/mnt/sanfs/APCF-PROD/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi", which > xinteract caused to be run in order to index the pepXML file that came > out of peptideProphet. When that crashed, xinteract exited - but > xinteract didn't crash, Perhaps a minor distinction, but as you > called it out it's probably worth clearing up. > > Brian > > On Wed, Jun 9, 2010 at 11:25 PM, Simon Michnowicz > <[email protected]> wrote: > > 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 spctools- > [email protected]. > >> > To unsubscribe from this group, send email to spctools- > [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 spctools- > [email protected]. > > To unsubscribe from this group, send email to spctools- > [email protected]. > > For more options, visit this group at > http://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 spctools- > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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