A quick Start Guide to Mnova MS

Learn how to get your first results in a few minutes

Please note that you can also check our Mnova MS Starting Video.

1. Drag&drop the raw file to Mnova in order to display the TIC (at the top of the window) and the MS spectrum of the highest signal.

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 just by clicking on the corresponding signal of the TIC. For example in this case, we have selected the spectrum number 467 at a 'Retention time' of 8.26 min:

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/Spectrum Selection Mode/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/Spectrum Selection Mode' menu.

5. It is possible to add another MS spectrum to the page, just just by clicking on the 'Append' button . Next, select the desired time span in the TIC in order to obtain the corresponding MS spectrum. In this case we have added the MS spectrum 738 which appears at 12.90 min.

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 files pasted in any page of the .mnova document, click on the 'Calculate Molecule Match' button of the toolbar  Then follow the menu 'View/Tables/Molecule Match' 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 this case, the best result is for the compound number 1 (C20H23N). You can see in the picture below the MICC (in green) over the TIC (in red):

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 (the number 467 in this case) 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' or select the corresponding option in the scroll down menu of the 'Elemental Composition' icon of the toolbar:

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

It will be possible to add more 'Element Constraints' just by clicking on this icon

Once you have finished with the constraints, click on OK and go back to the MS spectrum in order to click on the desired peak with the crosshair. Finally, follow the menu 'View/Tables/Elemental Composition' to get the results:

Finally, the user will be able to save , print  or export to PDF , the document by clicking on the corresponding icon in the toolbar.