Starting Guide to Mnova MSChrom


Learn how to get your first results in a few minutes with Mnova MSChrom:

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 zoom in to show details in in either the TIC or MS plots 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  Zoom In Icon

3. Select any other mass spectrum at a particular retention time with the crosshair feature Crosshair Icon just by clicking on the corresponding point on 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 range of the retention time (red rectangle in the picture below):

If you want to ‘CoAdd’ the whole peak, just select the mode ‘Peak’ under the ‘Mass Analysis/Spectrum Selection Mode’ menu and then click on the desired peak in the TIC.

To generate a ‘CoAdd’ of the whole peak with background subtracted, just select the mode ‘Peak (Background Subt.)’ under the ‘Mass Analysis/Spectrum Selection Mode’ menu, and click on the desired TIC peak.

5. Add another MS spectrum to the page, just by clicking on the 'Append' button . Next, select the spectrum as shown above. In this case we have added the MS spectrum 738 which appears at 12.90 min.

6. Molecule match analysis determines the possible presence of one or more given structures (or molecular formulae) within a mass spectral data set. The isotope cluster of each structure is computed and compared to each spectrum in the data set, and the mass spectrum with the best match that returns a score above the preset threshold is taken as a positive match. Otherwise it is taken as "Not found". Open an LC/MS data set, and open one or more structures. Click on the ‘Calculate Molecule Match’ button of the toolbar Calculate Molecule Match. Choose 'View/Tables/Molecule Match’ to open the Molecule Match Table. This table contains the status of each structure or formula - matched or not found, and other information such as Retention Time, Match Score, Adduct/Lose etc.


Click on any matched row in the table to display the Matched Isotope Cluster Chromatogram (blue curve), overlaid with the TIC. The blue vertical line indicates where the best match is.  The mass spectrum corresponding to that retention time (9.79 min in this case) is displayed with the predicted isotope cluster overlaid on it (the blue lines and the shaded area):


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 Element Constraints 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:

8. It is possible to predict the isotope cluster of a molecular formula with different adducts and losses, by following the menu 'Mass Analysis/Spectrum Prediction/Predict'.  Add or choose an MFs, click OK to simulate the isotope clusters with the pre-defined adducts/losses.  Next choose a mass spectrum that you want to analyze, and click on the row in the Mass Prediction Table with the desired Adduct or Loss to compare with the displayed mass spectrum.  For example, click the first row to show the predicted isotope cluster (blue lines) with H+ as the adduct:

Next click the 5th row to show the predicted cluster with NH4+ as the adduct:

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


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