Get Empowered: Empower User Question | Tip #222, Using the Compare Window in Empower

By April 21, 2021

Tip #222: Empower User Question: Aligning chromatograms using the Compare window in Empowerer

Welcome back to Get Empowered! In the last Empower tip-of-the-week blog for Empower Chromatography Data System, we learned about Durable Data (Tip #221).

In this week’s tip, we will answer an Empower user question regarding aligning peaks between chromatograms where the retention times have shifted.

Q: It is not unusual to have a small amount of retention time shifts from injection to injection. How can I be sure that the peaks from chromatogram to chromatogram are the same so that I can track them with this shift in retention time?

Great question. We can solve the problem using the Compare window.

Let’s get started.

Step 1

Highlight the channels of data, right click, and select ‘Compare’ (figure 1).


Figure 1

Step 2

The Compare window opens displaying an overlay of the chromatograms (figure 2).


Figure 2

Step 3

Click the ‘Individual Plot’ tool and a stack plot is displayed (figure 3).


Figure 3

Step 4

Click the ‘Alignment Markers’ tool to display the alignment markers in the chromatograms (figure 4).


Figure 4

Step 5

Move the ‘first marker to the first peak’ in each chromatogram and the ‘second marker to the last peak’ in each chromatogram (figure 5).


Figure 5

Step 6

Click the ‘Align Chromatograms’ tool to align the peaks (figure 6).


Figure 6

Step 7

Click the ‘Compare Main Window’ tool to display the aligned chromatograms in one window (figure 7).


Figure 7


It’s that easy!

Final Notes:

  1. If you zoom in on the baseline of the chromatograms after Step 6, the resulting view in Step 7 will remain zoomed in. This will help when looking at small impurity peaks.
  2. You can use either the Pro or QuickStart interface for this tip.


Please rate this Empower Tip of the Week

Next week in Empower Tip #223: We will resume our series on working with Export Methods (Part 3).

JOIN US for an Empower: Ask Me Anything Webinar on May 19, 2021

Neil will answer your questions about Processing Data.

Learn More and Register.

More Empower Resources:



Do you want Empower Tips sent to your inbox every week?

Subscribe Now

Questions? Tips of your own? Let us know!


Categories: Empower Tips