Wiff file conversion to mzML

[Jana Horáková]

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

[钟传奇]

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,

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[Xabier Martinez De Morentin]

Did you solved this????