Hi Everyone, Doing further diagnostics about the issue I realized that it is generating an error converting the Xtandem file to raw.pep.xml. Here is the error listed
RawData]$ Tandem2XML IPAS_0516_HCD_TCE_SG66to68.xtan.xml IPAS_0516_HCD_TCE_SG66to68.raw.pep.xml IPAS_0516_HCD_TCE_SG66to68.mzXML(1) : error 4: Syntax error parsing XML. If any one has sugessions to resolve this problem that would be highly appreciated. Thanks Amin On Thursday, February 19, 2015 at 3:26:32 PM UTC-6, matt.chambers wrote: > > Hi Amin, > > Actually it looks like X! Tandem is finishing fine. It's TPP's > InteractParser that is failing. I have no idea why, there no error > message. I'm cross posting this to the spctools-discuss mailing list. > They'll probably want to see the pepXML files from the "bad" X! Tandem > runs. > > -Matt > > > On 2/19/2015 3:16 PM, Momin,Amin A wrote: > > Hello Parag, > > I converted the thermo Qexactive raw files to mzXML using > msConvert. We have 24 files for the different fractions for the sample. > When I do a search for the batch of files with TPP X!tandem I was only able > to get search results for 5 fractions. We don't see similar issues with > search with the Orbitrap data. I have attached the tpp log files for one > successful run and one un-successful. Let me know if you need additional > information to help us diagnose this issue. > > > > Thanks > > Amin > > > > -----Original Message----- > > From: Parag Mallick [mailto:[email protected] <javascript:>] > > Sent: Thursday, February 12, 2015 6:34 PM > > To: Katayama,Hiroyuki > > Cc: [email protected] <javascript:>; Momin,Amin A > > Subject: Re: [proteowizard-support] Question about Qexactive RAW > > > > Hi Hiroyuki, > > > > Say hi to Sam for me. Can you please give us a little more information > about what the error is? Perhaps a screen capture of it? > > > > Also - are you using the newest version of msConvert? > > > > Thx. > > ~ Parag M ~ > > > > > > > >> On Feb 11, 2015, at 8:25 AM, Katayama,Hiroyuki <[email protected] > <javascript:>> wrote: > >> > >> Dear Customer support, > >> > >> We are Thermo mass spectrometry user and running proteomics analysis. > >> The machines are Orbi Elite and Qexactive. > >> We first generate MZXML from the RAW files and next searching with TPP > X!Tandem search engine. > >> > >> Orbi data always works fine but Qexactive data often shows error. > >> Could you please give us suggestions about this problem? > >> > >> Thank you very much. > >> > >> > >> Hiroyuki Katayama, Ph.D. > >> Scientific Manager > >> > >> The University of Texas, MD Anderson Cancer Center, Clinical Cancer > >> Prevention, Hanash Lab > >> 6767 Bertner Ave, Unit 1013, BSRB: S14.8116, Houston, TX 77030 > >> > >> e-mail: [email protected] <javascript:> > >> Phone: 713-563-1549 > >> > >> > >> ---------------------------------------------------------------------- > >> -------- Dive into the World of Parallel Programming. The Go Parallel > >> Website, sponsored by Intel and developed in partnership with Slashdot > >> Media, is your hub for all things parallel software development, from > >> weekly thought leadership blogs to news, videos, case studies, > >> tutorials and more. Take a look and join the conversation now. > >> http://goparallel.sourceforge.net/____________________________________ > >> ___________ > >> proteowizard-support mailing list > >> [email protected] <javascript:> > >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support > > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
