Get Empowered: Review Window and the Processing Method | Tip #113, ACQUITY QDa MS Data

By March 20, 2019

Tip #113: Working with ACQUITY QDa MS data in Empower Software (Part 13)

Welcome back to Get Empowered! In the last Empower tip-of-the-week post for Empower Chromatography Data Software, we learned how to create an MS spectra library from data collected with the ACQUITY QDa mass detector (Tip 112).

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

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

Part 2: Learning how to use the library to identify peaks in sample chromatograms.

Empower compares the Apex Spectrum from a peak to the spectra in the Library and determines if there is a match. And there are two ways to use the libraries 1) ‘manually’ by searching one spectrum from one peak at a time or 2) ‘automated’ by adding the Library search to the Processing Method.

This week we will look at the manual technique.

Let’s get started.

Step 1

Start by bringing data with the unknown peaks into Review. Once the Method Set has been opened and applied, select ‘Load Library’ from the Library menu. Highlight the Library you want to use and click ‘Load’ (figure 1).

Empower Tips: Bringing in data/loading library | Figure 1

Figure 1

Step 2

The Library spectra are loaded into Spectrum Review and you can see their names in the Spectra tab (reference back to Tip#112). Use the ‘Select Field’ to deselect all spectra, except the one you are interested in identifying (figure 2).

Empower Tips: Identify spectra by deselecting the spectra you do not want | Figure 2

Figure 2

Step 3

Select ‘Match Parameters’ from the Library menu (figure 3).

Empower Tips: Select Match Parameters | Figure 3

Figure 3

Step 4

There are two parameters which can be set for Spectral Matching.

  1. Search Depth tells Empower to report a number of possible matches from best to worst case. The default value is 3 and the maximum is 9.
  2. Retention Time Presearch Qualifier instructs Empower to look at the Retention Time of the spectrum in question and compares it to the Retention Times of the spectra in the Library before any spectral comparison is done. There is a range set by the RT Window (%).

For example: if the Retention Time of the peak is 1 minute and the RT Window (%) is 10 (default), the range is 57 to 63 seconds. When Empower looks at the Retention Time of the first spectrum in the library, if that value is within the range then the spectral comparison takes place. If not, that spectrum is removed from the search list and Empower moves on to the next spectrum.

Once the parameters are set click ‘OK’ (figure 4).

Empower Tips: Set parameters | Figure 4

Figure 4

Step 5

Select ‘Match Against Library’ (Library name, in this case MS Library 1) from the Library menu (figure 5).

Empower Tips: Select Match Against Library | Figure 5

Figure 5

Step 6

Select the ‘Library Match’ tab under the Spectrum Review window to view the results. The higher the Match Score, the better the match. Therefore, the best match to the spectrum from the peak matches best to the called Black Cohosh 67. You can also see the Library spectra in the plot (figure 6).

Empower Tips: Library Match to view the results | Figure 6

Figure 6

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 #114– We will continue this series on working with ACQUITY QDa MS data in Empower (Part 14).



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Categories: Empower Tips