Empower Tip: Review Window and the Processing Method

In this tip, we will continue our series on working with ACQUITY QDa MS data in Empower (Part 3).

Picking up where we left off in the Mass Analysis window at the end of Tip 100, let’s identify the various parts of the window and the default displays.

The upper area displays the ‘Apex UV’ and ‘MS Spectra’ for every integrated peak (default view).

Below the MS Spectra, the UV Chromatogram is displayed.

Below the UV Chromatogram is the MS TIC plot (TIC means Total Ion Chromatogram). This plots each point in time as the sum of all ion intensities across the collected mass range. In this case, there were two scans and both TIC plots are overlaid.

Finally, the lower chromatogram is an overlay of the Extracted Ion Chromatograms of the prominent mass in the higher responding polarity for each peak.

The ‘Combined from the Spectrum View menu’, displays the ‘Apex Spectrum’ and the ‘Combined Spectrum’ for every integrated peak.

The ‘Combined Spectrum’ is an averaged spectrum taken across a section of the peak which enhances the Signal to Noise ratio. This section of the peak is determined from the ‘Combined Peak Spectra % Peak Height Threshold’ which is set on the MS 3D Channel tab of the Processing Method. If we set that to ‘0’, Empower uses all of the spectra from peak start to peak end. If we set that to ‘30’, Empower uses the spectra from 30% of the peak height. (The default value when making a new Processing Method is 10.)

Selecting ‘Purity’ from the Spectrum View menu shows the ‘Leading Edge Spectrum’, ‘Apex Spectrum’, and ‘Trailing Edge Spectrum’ for every integrated peak.

Viewing the spectra in this way provides evidence of peak homogeneity. The points at which Empower takes the ‘Leading’ and ‘Trailing Edge Spectra’ are determined from the ‘Leading Spectra Extraction Point (%)’ and the ‘Trailing Spectra Extraction Point’ which are set on the MS 3D Channel tab of the Processing Method. If we set the Leading Spectra Extraction point to ‘0’, Empower takes the spectrum at peak start. If we set the value to ‘30’, the spectrum is taken 30% of the way from peak start to the retention time of the peak. The same is true of the ‘Trailing Spectra Extraction Point’. We can see the spectra for the second peak at 1.2 minutes are not consistent across the peak.

It’s that easy!