GC Image User Forum

It seems like the MS data binning is not working. I'm working with HR data, yet none of the non-integer options results in a binned spectrum with the accurate mass (see attachment).

There are two MS spectra shown, one (blue) is from Profile data linked, another (red) is from MS data of the image (either Blob, Peak, or Point). Sometimes MS data of the image may not be HRMS. This depends on the original raw data that the image was imported from. For example, importing an Agilent MassHunter QTOF .D folder that contains only profile data will result in an integer-MS image with a HRMS profile data linked.

You can check this by switching to Point MS mode and clicking on the chromatogram to view a point spectrum. If the point spectrum has only integer m/zs, then MS binning setting does not matter.

The point MS data is also only integer values. I'm importing from and HDF5 file (Tofwerk) - is there any way to get non-integer image data from this file format? If not, for which file format/vendor format do you support non-integer binning?

In general, any raw data file of Agilent MassHunter and Jeol that contains centroided data will work. But TofWerk's HDF5 files only contain profile and integer MS data instead of centroided data.

Currently you can use:

File > Export Image > Export Profile Data to Centroid

, to export centroided data to a CDF file, and then re-import it back.

BTW, in next release (R2.7), we have made this process simpler by exporting directly to an image (GCI) file without re-importing. An alpha version will be available for testing soon.