MSConvert parameters for mzml files

[volkan yildirim]

Hi all,

I am trying to convert .wiff files to .mzml files for analysis. If I use SearchGui for conversion analysis works without a problem.  (I start the analysis with SearchGui but stop it when the wiff to mzml conversion finalizes) However if I use MSConverGui for conversion of wiff to mzml analysis does not work. So does anybody knows which MSConvert parameters are used in searchgui for the wiff to mzml.

Best ,

Volkan

[Harald Barsnes]

Hi Volkan,

Sorry for the very late answer! Seems like there was an error in the notification system for the Google group and I did not see your message until now.

When selecting a wiff file in SearchGUI you can see and edit the msconvert parameters by clicking the cog wheel next to msconvert. The msconvert command line used is also printed to the SearchGUI log file located in the resources folder next to the SearchGUI jar file.

Best regards,

Harald