Empower Tip: QDa MS Data in Empower

In Tip 357, we briefly looked at the Mass Analysis window. In this tip, we begin to look at the details in this window.

Let’s see how it’s done!

The Mass Analysis Window is used to view and analyze both PDA and MS spectra along with chromatographic data from a single result. Let’s first identify the default plots within the window.

Plot 1 displays the apex UV and MS spectra for every integrated peak.

Plot 2 displays the UV chromatogram.

Plot 3 displays the MS TIC plot. In this example, there was a positive scan and a negative scan, and TIC plots for both are overlaid.

Plot 4 displays an overlay of the Extracted Ion Chromatograms (XIC) of the prominent mass in the higher responding polarity for each peak.

Selecting Combined from the Spectrum View menu shows the MS apex spectrum and the MS 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. That 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 then Empower uses all of the spectra from peak start to peak end. If we set that to 30 then 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 both UV and MS, 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, then Empower takes the spectrum at peak start. If we set the value to 30, then the spectrum is taken 30% of the way from the peak start to the retention time of the peak. The same is true of the Trailing Spectra Extraction Point. NOTE: As shown previously in Figure 4, notice the spectra for the second peak at 1.2 minutes are not consistent across the peak.

It’s that easy!