Creating MS Method

Creation of the MS method consists of adding compounds to the MS Method table. In processing the compounds, it strongly depends on the fact whether the compound is identified as a peak on TIC (or another selected "standard" signal) or not, and on the usage of spectral libraries.

Using spectral libraries - compounds visible in TIC

When a spectral library is available (for example, the Demo_MS library included with the Demo_MS project), you can create an MS method. Clarity offers three search options:

Single Compound Search: Locks the mouse to the graph so you can select a peak to search for in the library.
Automatic Compound Search: Automatically searches all peaks identified in the TIC.
Target Compound Search: Searches the chromatogram for a compound whose spectrum exists in the library.

After selecting a search function, the corresponding dialog or tab will appear. For details, see the instructions for that specific dialog.

In either case, one or more compounds are added to the MS method using the names found in the library.

Using Spectral Libraries - compounds not visible in TIC

You can also add peaks that are not visible or identified in the TIC to the MS Method. To do this, you will usually need to useTarget Compound Search or locate the peak position for a known m/z value.

To extract a temporary signal at a given m/z, use the MS – Add Selected m/z Signal or MS – Add Selected m/z Signal – Manual… command. This lets you choose the m/z in the spectra graph or enter it directly in a dialog. Then zoom in on the found peak in the graph and runSingle Compound Search .

If you have selected too many temporary signals, you can hide them using MS – Remove Selected m/z Signals.

Not using Spectral Libraries

When spectral libraries are not used, adding compounds to the MS Method is slightly different. Instead of Single Compound Search or Automatic Compound Search, use theMS - Add Compound w/o Library Spectrum… command.

This opens the Add Compound w/o Library Spectrum, where you can:

Select the retention time of the desired compound in the chromatogram (interactively in the graph).
Enter the compound name.

The compound is then added to the MS Method Table, with its Library column left blank.

Note:

Some of the functions in the Result Table will not work for compounds that do not have a compound from spectral library linked. These include the comparison of expected and actual relative intensities for reference ions, as well as compound Conformity.

Using non-MS signals (e.g. PDA)

If you want to add a compound quantified using a non-MS signal measured within an MS configuration (for example, a PDA signal), follow the procedure described in this Working with non-MS Signals (e.g. PDA) on MS Instrument chapter.