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 [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.
