To begin, open the data analysis software. At the top left corner, click on the file button and select open. To select the files of choice, right click on the file name and select properties.
Then select calibration status. At the dropdown box, select internal calibration for the mass spectrometer. Ensure that all errors are less than one parts per million.
After that, select internal mobility calibration and confirm that the error is less than one part per million. Next, right click on chromatogram and select edit chromatogram. At type, click the dropdown box and select extracted ion chromatogram.
Under filter, select all MS, and for scan mode, select all to view the peaks for the molecule of interest rather than only its fragments. There are two filter options for molecule selection, masses or formula. If masses is selected, choose the theoretical M over Z of the molecule of interest, which in this case is 829.7985.
If formula is selected, choose the formula for the molecule and the ion forms of interest, which in this case is ammonium. For width, select plus or minus one. For polarity, ensure that it maintains the positive mode.
Under mobility, select 1.455 to 1.465 to isolate the molecule of interest and filter out molecules not falling within these values. Once the parameters are selected, click change followed by okay at the top right. After a brief time, the software will process the selections and output a chromatogram.
Right click at the baseline of the origin of the peak of interest and drag while holding to the end of the peak to obtain a live mass spectrum of fragments within that retention time. Right click at the left of the screen on mobilogram and select edit mobilogram. A window named edit mobilogram traces will appear.
Follow the steps demonstrated previously. For retention time, input the retention time of the peak of interest. Once the parameters are selected, click add, and okay at the top right.
Wait till the software processes the selections and outputs a chromatogram. For extracting ions, repeat the steps demonstrated previously until a list of ions is formed. At the bottom of the MS window, select profile MS and fragment MS to allow a spectrum view of ions from a full scan and passive.
For the spectrum view, right click and select copy compound spectra. The spectrum data that appears at the right can provide more information on the compound, such as resolution resolving power, intensity, and signal-to-noise ratio. To process the data, manually integrate the chromatogram and mobility peaks to yield valuable information on the molecule of interest.
Right click find and select compounds manually chromatogram or mobilogram. Left click and highlight the desired peak. The obtained information includes retention time, area, signal-to-noise ratio, and mobility.
