First Steps with the MSChrom Plugin

It is very easy to obtain your first results with the MSChrom plugin of Mnova:

1. Drag&drop the raw folder to Mnova in order to display the TAC (at the top of the window), the TIC (in the center) and the MS spectrum of the highest signal (this default can be changed from the 'Preferences/Mass/Setup')

2. You can expand any scale (in either the TIC or MS) by using the 'zoom in' feature, which can be accessed by just pressing the 'Z' key or by using the corresponding icon of the toolbar .

3. You can select any other mass spectrum for a particular time point with the crosshair feature  (press ESC key to keep the desired MS plot). For example in this case, we have selected the spectrum number 467 at a 'Retention time' of 8.26 min:

NOTE: The "Live Mass Spectrum Preview" preference will allow you to show the extracted mass spectrum on the fly when you hover the crosshair over the chromatogram (or trace). 

4. If you need to average the mass spectra over a certain time range (CoAdd), just select the crosshair, hold down the left mouse button and drag over the appropriate time span in the TIC. A label at the top of the MS will inform you about the spectrum ranges (red rectangle in the picture below):

If you want to 'CoAdd' the whole peak, just follow the menu 'Mass Analysis/Crosshair/Peak' and finally select the desired peak in the TIC.

To generate a 'CoAdd' of the whole peak without the tail-peaks just select the mode 'Peak (Background Subt.)' under the 'Mass Analysis/Crosshair' scroll down menu.

5. You can add another MS spectrum to the page, just by clicking on the 'Append' button . Next, select the desired time span in the TIC in order to obtain the corresponding MS spectrum.

6. The 'Molecule Match' is very useful to see if a mass spectrum and a chromatogram match with one of the molecular structures of the document. With the TIC and the mass spectrum displayed on the screen and some .mol or .sdf files opened in the .mnova document, click on the 'Calculate Molecule Match' button of the toolbar .  The 'Molecule Match' table will be displayed to see the results. This table will contain information about the 'Retention Time', Scan (number of spectrum), Match Score...  

Clicking on any molecule will display the MICC (Molecular Isotope Cluster Chromatogram), overlaid with the TIC.

In addition, Mnova shows you in the chromatogram the retention time of the match (with a blue vertical line) and displays the corresponding MS spectrum overlaid with the theoretical one (in green at a M/Z around 278, in this case).

7.  If you are using high resolution MS, it is possible to do an 'Elemental Composition' analysis of any peak of the Mass spectrum. First of all, follow the menu 'Mass Analysis/Elemental Composition/Constraints':

This will open the 'Elemental Composition Constraints' dialog box:

Click on this icon to add more 'Element Constraints'. Once you have finished with the constraints, click on the 'Elemental Composition' icon and select with the crosshair the desired peak of the Mass spectrum. A table with the results will be displayed (you can find this table under the 'View/Tables' menu). All the results obtained will satisfy the composition, DBE, and tolerance constraints, and will be ranked in decreasing order of fitness. Please bear in mind that a fitness value of 1 will be the perfect match.

8.  Follow the menu 'View/Tables/Parameters' to display and report the 'Parameters table' :

Finally, the user will be able to save , print or export to PDF , the document by clicking on the corresponding icon in the toolbar (or under the 'File' menu).