Spectrum Selection Mode

This feature will allow you to add additional MS spectra to your document and also to generate 'CoAdds' and subtractions.

Append: it will allow you to add additional MS spectra to the main window just by selecting 'Append' in the corresponding menu and clicking with the crosshair on the corresponding signal of the TIC. If the 'Append' option is not selected, the current MS spectrum will change after having clicked on the corresponding signal of the TIC.

In this case we have added the MS spectrum 738 which appears at 12.90 min.

You can combine the 'Append' option with the different modes of the crosshair (Manual, Peak, Peak (Background Subt) and Customized Peak):

Manual: This is the default mode of the crosshair. In this mode, 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 at a 'Retention time' of 8.64 min:

If you need to average the mass spectra over a certain time range (CoAdd), just hold down the left mouse button (after having selected the crosshair) 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):

After having done the 'CoAdd' you can do a 'subtraction' by just selecting the 'Crosshair' feature, pressing the 'SHIFT' key and holding down the left mouse button and dragging over the desired time span in the TIC.

Peak: Selecting this mode and clicking with the crosshair on the corresponding signal of the TIC, will generate a 'CoAdd' of the midle part of the peak. The spectra from the middle half are used because they’re the highest intensity and s/n.  Spectra at the peak edges are then the opposite, lower s/n and more likely to contain background. Often when a peak elutes, background is actually suppressed, especially with higher concentration components.  This approach is a common technique.

Peak (Background subt.):

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 and click with the crosshair on the desired signal of the TIC. You can do a 'subtraction' of any other chromatogram region just by selecting the 'Crosshair' feature, pressing the 'SHIFT' key and holding down the left mouse button and dragging over the desired time span in the TIC.

When you are in the spectrum selection mode (with the append mode disabled), you can choose graphically (by checking the blue circle ) which of the plots must be replaced when you select a spectrum in a chromatogram. The selection target can be also done from the MS Browser, just by selecting the applicable MS and clicking on the 'selection' button .

Customized Peak: This mode selects a peak of a chromatogram, integrates a percentage of the MS scans of the peak and automatically subtracts some scans before/after this peak. The implementation ensures that the integration has at least one MS scan.

If the selection is made with a point, this crosshair mode checks that the selected retention time point is within the peak limits. If it is not, the mode does nothing. Otherwise, the integration/subtraction is performed with the selected peak.

If the selection is made with a range, this crosshair mode checks that the selected retention time range has any peaks. If it does not, the mode does nothing. Otherwise, the mode selects the most intense peak in the range (highest height) and performs the corresponding calculations.

This mode can be configured from the the Customized Peak Settings dialog. From here, you can modify the percentage of peak integration (from 1% to 100%) and the peak reference (From Start (the first MS scans), Near Top (the MS scans nearest to the top of the peak) and To End (the last MS scans).

Also, the user can indicate the number of scans before/after the peak to be subtracted (zero or a positive integer). These setting are saved to the Mnova configuration (Registry Editor in Windows), so they are independent of the Mnova document.

You can move forward/backward scan by scan by clicking the buttons "Previous Scan" or "Next Scan" in the ribbon menu, or by using the shortcuts Alt+Left or Alt+Right arrow:

Set Merge Tolerance: From this dialog box, you can select the tolerance (in Da or ppm) of the coadded mass spectra.

Merged tolerance is a m/z tolerance used any time mass spectra are summed or subtracted. The tolerance is applied to m/z values. Thus a merge tolerance of 0.1 Da means that if two spectra being summed contain, respectively, m/z 100.100 and m/z 100.150, the two mass peaks with be logically summed, since they’re within 0.1 Da. The resultant intensity is the simple sum; the resultant m/z value will be the intensity-weighted average of 100.100 and 100.150.

Select MS/UV together: When having this button pressed, if you select a position or a range in either the TIC or DAD trace, the MS spectrum and the UV spectra will be extracted at the same time.

Select and Deconvolute: If this mode is enabled (in the crosshair mode) the extracted spectrum gets also deconvoluted in the same step.

Live Crosshair: it will temporarily activate the 'Live view' mode which will display the applicable MS spectrum when hovering the 'crosshair' across the chromatogram.

The 'Live Mass Spectrum Preview' option is also available under the 'File/Preferences/Mass/General' dialog box.

The 'Correlated Crosshair' mode will display the crosshair as usual in the active plot and also as a semi-transparent crosshair in the none-active plots of the same type (chromatograms, mass spectra or UV spectra):

Select Manually: That will allow you to get (or subtract) the MS (and UV) spectrum at the desired retention time (or scan) range.

In the subtract mode, you can select multiple spectral ranges from the applicable scroll down menu.

Find Fragment ion spectrum: to easily display the applicable MS/MS spectrum from a MS dataset of the precursor, by matching the highest mass peak at around the same RT value. The highest mass peak in the MS spectrum depends on the displayed range, so if you make a zoom, the m/z value will be taken from the highest displayed peak.