Time for scan X greater than scan Y
This is the default converting action of protoWizard. You will need to load the the not graphical user interface (GUI) version of the converter, msconvert.exe. Using a line somthing like the following in the dos prompt:
- Code: Select all
msconvert D:\Data\MyFile.RAW --filter "sortByScanTime" --mzXML -o D:\Data\Output\
Currently, version 2.2, the "sortByScanTime" option is only avaiable in the command line version of the software and has not been ported over to the GUI yet.
Hint: If you're using MassLynx you can load up the run list and have it automatically run the converter on each file:
1) Open MassLynx and above the Sample Table select Samples → Format → Customise. Enable the following Fields to display
2) Choose Samples → Format → Save and save the new Sample List format.
3) Make sure that MassWolf/msconvert is in the MassLynx directory. Choose massWolf/msconvert from the Process drop down list. As massWolf/msconvert is a command-line tool it requires some parameters to make it function. In the below example the following line has been added to the 'Process Options' column;
massWolf add: --mzXML C:\MassLynx\Default.pro\Data\1234.raw
msconvert add: D:\Data\MyFile.RAW --filter "sortByScanTime" --mzXML -o D:\Data\Output\
4) To process data that has already been acquired use the usual MassLynx Run (play) icon and select “Auto Process Samples”. When processing starts a command prompt will open when required and will output the mzXML file into the parent folder.