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
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