Get Empowered: Review Window and the Processing Method | Tip #114, ACQUITY QDa MS Data

By March 27, 2019

Tip #114: Working with ACQUITY QDa MS data in Empower Software (Part 14)

Welcome back to Get Empowered! In the last Empower tip-of-the-week post for Empower Chromatography Data Software, we learned how to use a MS Spectra Library to identify spectra from unknown peaks via the manual technique. (Tip  #113).

Working with ACQUITY QDa MS data in Empower:

  • #100: How to view the base mass and mass spectra for the peaks in a chromatogram
  • #101: How to work with 2D ACQUITY QDa MS data
  • #103: Viewing different spectral views in the Mass Analysis window
  • #104: Extracting chromatograms and spectra while working in the Mass Analysis window
  • #105: Why it is important to align chromatograms when collecting data from both a PDA and a ACQUITY QDa mass detector
  • #106: How to optimize sensitivity by extracting a single mass rather than working with a TIC plot
  • #107: How to smooth the chromatogram using the Processing Method
  • #108: How to smooth the chromatogram using a Derived Channel in the Method Set
  • #109: How to track peaks using the ACQUITY QDa mass detector
  • #110: Using CODA (component detection algorithm) as a tool when scouting for peaks
  • #111: Using MS 3D subtraction to remove background interference
  • #112: How to create a MS Spectra Library from data collected with the ACQUITY QDa mass detector
  • #113: How to use a MS Spectra Library to identify spectra from unknown peaks via the manual technique

This week, we will continue our discussion on creating and using MS Spectral Libraries.

Part 3: Learning how to automate the library to identify peaks in sample chromatograms.

The first benefit of doing it this way is that Empower will automatically take the apex spectrum of every integrated peak and compare them to the spectra in the library. The second benefit is that you can search against multiple libraries.

In this tip, we will look at the automated technique.

Let’s get started.

Step 1

We start by bringing data with the unknown peaks into Review. Once the Method Set has been opened and applied, go to the Processing Method and click the ‘MS Library Search’ tab (figure 1).

Empower Tips: Open the MS Library Search’tab | Figure 1

Figure 1

Step 2

The default settings are displayed when you make a new Processing Method. Let’s first understand what these settings are and we can use them accordingly.

  • Search Depth has a maximum of 3 – Refer to Tip #113 for a more detailed description
  • Start Mass and End Mass – Limits the search to Library spectra with masses within the specified range.
  • Noise Threshold % – Removes noise from spectral data before a Library search. The threshold value is applied as a percentage of the Base Peak intensity. Mass intensity values in the sample spectrum less than the Threshold value are set to zero.
  • Spectra to Average – Number of spectra to be averaged to produce the extraction. When spectra are extracted, they can be averaged over a series of scans to reduce the noise level in the spectra. For example, a value of 1 indicates no averaging. A value of 3 averages the extracted spectrum with the spectrum on each side of the extracted spectrum.
  • Combine Method – Indicate how to combine a spectrum: ‘Average’ averages the intensities of the spectrum and ‘Sum adds the intensities of the spectrum.
  • Noise Baseline – A value that specifies in minutes how Empower software calculates a baseline spectrum. When you enter a range, Empower Software averages all spectra in the specified time ranges to produce a noise spectrum, which is subtracted from any extracted spectra.
    Refer to Tip #111 which discusses MS 3D Subtraction for information on entering the time values and the description of the Multiplier.
  • Library List – select the Library or Libraries you want to use.
  • Peak Separation – Binning value to apply to the baseline-corrected spectrum. Empower Software bins the extracted and combined spectrum at the resolution in this field.
  • Retention Time Presearch – Refer to Tip #113 for a more detailed description

Step 3

Once you have made the appropriate selections be sure to save the Processing Method (figure 2).

Empower Tips: Save the Processing Method | Figure 2

Figure 2

Step 4

Reapply the Method Set. We now see the results in the Peaks table under the chromatogram. This information will be part of the result (figure 3).

Empower Tips: Reapply the Method Set | Figure 3

Figure 3

Step 5

Go to the Results window and click the ‘MS Library Match’ tab. Here we see the three results for the peak with the best match (the highest MS Match Score) at the top of the list (figure 4).

Empower Tip: Results window/open the MS Library Match tab | Figure 4

Figure 4

It’s that easy!

Final notes:

  • This procedure can be followed using the QuickStart or Pro interface.
  • ACQUITY QDa Mass Detector is compatible with the Alliance HPLC system.


Please rate this Empower Tip of the Week

Next week in Empower Tip #115– We will continue this series on working with ACQUITY QDa MS data in Empower (Part 15).


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Categories: Empower Tips