Using MS Data Converter to Centroid a WIFF File for Importing into the XCMS Software

For research use only. Not for use in diagnostic procedures.

Answer

The metabolomics platform XCMS from Scripps University can only process mass spectrometry data that is centroided, so data files from SCIEX instruments originally acquired in profile mode must be converted to the centroid format. To do this, the wiff file is converted to a mzML file using the MS Data Converter program (Win 10 compatible), which is freely available on our Software Downloads page. 

After the installation of MS Data Converter is complete, the selected wiff file can be converted following these steps:
1) Find the folder where the MS Data Converter software was installed: C:\Program Files\AB SCIEX\MS Data Converter or on a 64-bit system the directory is C:\Program Files (x86)\AB SCIEX\MS Data Converter.
2) Create a new text file in this folder and name it “Example batch file.bat”. Your computer may be set so that file extensions are not shown for known file types. Select the View tab and then select the Details option under the Layout section. Ensure that the file you created is listed as MS-DOS batch file and not a text document.
3) Open the batch file in a text editor such as Notepad or WordPad to enter the command line instructions as detailed in the command line syntax section. Adding a pause command on the next line of the batch file is recommended. This will keep the command window open, which will allow you to see error messages in the event of incorrect syntax.
4) Once the correct syntax is constructed, save the batch file, close it, and then run the conversion by double clicking on the closed file.

Here is an example for a file conversion to mzML in centroid mode:
AB_SCIEX_MS_Converter WIFF "D:\Data\File A.wiff2" -centroid MZML"D:\Data\File A.xml"

The generic command line syntax to use the tool is:
AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]