Hello Amin, It is somewhat telling that only the QExactive runs fail, and the Orbitrap ones are okay. Can you share files from a couple of cases so I can have a look? You can send the files or a link directly to me. Cheers, --Luis
On Fri, Feb 20, 2015 at 3:20 PM, Amin Momin <[email protected]> wrote: > 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]] >> > Sent: Thursday, February 12, 2015 6:34 PM >> > To: Katayama,Hiroyuki >> > Cc: [email protected]; 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]> 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] >> >> 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] >> >> 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. > -- 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.
