Get Empowered: Review Window and the Processing Method | Tip #59, Deriving Channels

By March 7, 2018

Tip #59: Deriving Channels in Empower (Part 12)

Welcome back to Get Empowered! In our last tip-of-the-week blog for Empower Software, we reviewed Deriving Channels when working with 3D MS chromatography data in Empower.

  • Tip 47: Smooth a chromatogram by Deriving a Channel (part 1)
  • Tip 48: Correct for the time offset between detectors connected in series by Deriving a Channel (part 2)
  • Tip 49: Subtract a baseline from a 2D chromatogram by Deriving a Channel (part 3).
  • Tip 51: Subtract a 2D baseline from 3D PDA data by Deriving a Channel (part 4).
  • Tip 52: Derive MaxPlot from 3D PDA data (part 5)
  • Tip 53: Derive TotalPlot from 3D PDA data (part 6)
  • Tip 54: Derive RatioPlot from 3D PDA data (part 7)
  • Tip 55: Derive Timed Wavelength from 3D PDS data (part 8)
  • Tip 56: Derive Single Mass from 3D MS data (part 9)
  • Tip 57: Derive TIC plot from 3D MS data (part 10)
  • Tip 58: Improve noisy TIC plot Derived from 3D MS data (part 11)

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.

Step 1

We begin by bringing a channel of 3D MS data into Review (Figure 1).

Empower Blog: 3D MS data into Review | Figure 1

Figure 1

Step 2

Go to the Method Set window and Derive a Channel, selecting MS: MaxPlot (Figure 2).

Empower Tip: Select MS:MaxPlot | Figure 2

Figure 2

Step 3

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

Empower Tips: Enter Start Mass and End Mass/ Select the MS Scan | Figure 3

Figure 3

Step 4

Save the Derived Channel and select a Processing Method (Figure 4).

Empower Tips: Save Derived Channel / Select a Processing Method | Figure 4

Figure 4

Step 5

Return to the Main Window and apply the Method Set. The MaxPlot chromatogram is displayed (Figure 5).

The MaxPlot appears to be a bit noisy. Can this be improved? Yes, by employing CODA.

Empoer Tips: MaxPlot chromatogram is displayed | Figure 5

Figure 5

Step 6

Return to the Method Set window, right-click on the Derived Channel in the tree, and select Properties (Figure 6).

Empower Tips: Right click on Derived Channel /Select Properties | Figure 6

Figure 6

Step 7

Click the MS CODA tab, enable CODA, and click OK (Figure 7).

Empower Tips: Click MS CODA tab / Enable CODA | Figure 7

Figure 7

Step 8

Return to the Main Window, re-apply the Method Set and notice the improvement in the MaxPlot chromatogram (Figure 8).

Empower Tips: Improvement in the MaxPlot chromatogram | Figure 8

Figure 8

It’s that easy!

Final note: This procedure can be followed using the QuickStart or Pro interface.


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Next week in Empower Tip #60: Deriving Channels in Empower (part 13).


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