MS1 Scan Summing
MS1 (isotope plot) scan summing enables users to view less abundant peaks more clearly so that they can confidently make peak assignments.
The new Sum MS1 icon on the plot widget is a local per-peptide summing option rather than a
global per-project setting. If a user switches to a new peptide, it will default to single scan data,
but the summing setting will be preserved for the previous peptide. If summed scans are enabled,
changing the XIC start and end times (whether through dragging the limits in the XIC plot, or
right-clicking on a peptide and setting the XIC time interval) will recalculate and reload the
summed MS1 spectrum.
MS2 Scan Summing
Combine MS2 spectra (MS2 and mass error plots only) sums the MS2 Plots for all the peptides
for a selected row in the Peptides table. The title of the plot updates to show the counts of the
peptide scans in the combined MS2 plot:
To enable Combine MS2 spectra, right click in the MS2 plot and select Combine MS2 spectra from the menu:
The advanced command Combined MS/MS Spectra configures the number of summed spectra (averaged spectra to be annotated with the MS/MS fragments). Changes to this count can be made after processing to modify the results.