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 on TIC
When there is a library present (you can use the Demo_MS library packed with the Demo_MS project), it is possible to create the MS method. Use either Single Compound Search (locks the mouse to the graph and lets you select the peak for which you want to perform the search), Automatic Compound Search (performs the Automatic search on all peaks identified on the TIC) or Target Compound Search (looks the chromatogram for a compound which has spectrum i the library) function. Appropriate dialog/tab appears, please see the description of work with that particular dialog:
Either way, one or more compounds are inserted in the MS method, with the name found in the library.
Using Spectral Libraries - compounds not visible on TIC
You can, of course, add other peaks which are not visible/identified in the TIC to the MS Method too. To do so, you will probably need to use the Target Compound Search or find the position of the peak on some particular m/z you know. To extract a temporary signal on the given m/z, use the MS – Add Selected m/z Signal or MS – Add Selected m/z Signal – Manual… command. This will allow you to select the m/z in the spectra graph or directly set it in the special dialog. Zoom to the found peak in the graph and use the Single Compound Search function. If too many temporary signals are selected, you can hide them by using MS – Remove Selected m/z Signals command.
Not using Spectral Libraries
When you are not using Spectral Libraries, the procedure of adding compounds to the MS Method is slightly different. Instead of using the Single Compound Search or Automatic Compound Search functions, the MS - Add Compound w/o Library Spectrum… command should be used instead. It will invoke the Add Compound w/o Library Spectrum dialog which allows you to set the retention time where the desired compound is found in the chromatogram (selected interactively in the graph) and the name of the compound, after which it will be added to the MS Method Table. The Library column for such compound will be 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.