I tried the ProteoWizard but it did not work. The following error message appears in TPP.
*EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem.params * X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) Loading spectra (mzParser)............................... loaded. Spectra matching criteria = 60476 Pluggable scoring enabled. Starting threads . This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. command "c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem.params" failed: No such process *Command FAILED* RETURN CODE:768 Command 2 [Wed Sep 3 13:29:11 2014] [ Show / Hide ] *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\Tandem2XML c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem.pep.xml * Failed to open input file 'c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem'. command "c:\Inetpub\tpp-bin\Tandem2XML c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem.pep.xml" failed: Operation not permitted *Command FAILED* RETURN CODE:256 On Wednesday, September 3, 2014 10:24:19 AM UTC+2, Robert wrote: > > Hi Jana, > > Did you try already the ProteoWizard (msconvert) for conversion? It has an > option for TPP compatibility. > > Best, Robert > > On 03.09.2014 02:29, Jana Horáková wrote: > > Hi, > I would like to use TPP with Tandem to generate pepXML. I have encountered > a problem when trying to do the database search of my mzML file. I used the > AB Sciex MS Converter (release June 2012) and the batch command > > AB_SCIEX_MS_Converter WIFF "C:\AB SCIEX\ProteinPilot Data\Data\E1m.wiff" > -centroid MZML "C:\AB SCIEX\ProteinPilot Data\Data\E1m.xml" /index > /nocompression > Pause > The conversion finishes without problems. > > I tried leaving out /index /nocompression or generating -profile MZML > with the same outcome in TPP. The error message is pasted below. > > X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) > > Loading spectra (mzParser).c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.mzml(1) > : error 2: Syntax error parsing XML. > > command "c:\Inetpub\tpp-bin\tandem > c:/Inetpub/wwwroot/ISB/data/140728_JB_E1m.tandem.params" failed: Unknown error > > *Command FAILED* > RETURN CODE:63744 > > Do you have any suggestions on how to solve the problem? > > Thank you, > Jana > -- > 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 spctools-discu...@googlegroups.com <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
