Empower Tip: Review Window and the Processing Method

In this tip, 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.

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’.

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.

Select ‘Match Parameters’ from the Library menu.

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

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.

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’.

Select ‘Match Against Library’ (Library name, in this example is ‘MS Library 1’) from the Library menu.

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.

It’s that easy!