Empower Tip: Review Window and the Processing Method

In this tip, we will discuss another option for Deriving Channels when working with 3D MS data, called MaxPlot

You may recall that we learned about MaxPlot for 3D PDA data in Tip 52. Today we are going to learn about MaxPlot for 3D MS data. MaxPlot is a 2D chromatogram that plots each time point at the maximum intensity across the mass range. MaxPlot is Empower's term for the channel of data commonly referred to in mass spectrometry as the BPI (Base Peak Intensity) channel. It uses only the intensity of the most intense peak (base peak) at a given retention time, contrary to the TIC which takes all ions into account.

Let me show you how it is done.

We begin by bringing a channel of 3D MS data into Review.

Go to the Method Set window and Derive a Channel, selecting MS:MaxPlot.

Enter the Start Mass and End Mass and select the MS Scan (3D channel) from the Function drop down list.

Save the Derived Channel and select a Processing Method.

Return to the Main Window and apply the Method Set. The MaxPlot chromatogram is displayed. The MaxPlot appears to be a bit noisy. Can this be improved? Yes, by employing CODA.

Return to the Method Set window, right click on the Derived Channel in the tree and select Properties.

Click the MS CODA tab, enable CODA and click OK.

Return to the Main Window, re-apply the Method Set and notice the improvement in the MaxPlot chromatogram.

It’s that easy!