Here is my way to process wiff files. First, wiff files were converted to mzML files using msconvert (AB Sciex). Second, mzML were converted to mzXML files using proteowizard MS convert. Finally, mzXML were searched using Xtandem.
Hope this help. Best, On Wed, Sep 3, 2014 at 3:53 PM, Jana Horáková <jane.ho...@gmail.com> wrote: > Hi, > I want to use TPP (Tandem) to generate pepXML out of my wiff files. I have > encountered a problem when trying to do a database search of my mzML file. > I used AB Sciex MS converter (release June 2012) with the following batch > command to convert my wiff files to mzML. > > 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 > > I tried leaving out /index /nocompression or doing a -profile MZML > conversion with the same outcome in TPP. The error message is pasted below. > > *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).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 > > Thank you for any suggestions. > > 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-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. > -- 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.
