Isotopically resolved data requires a set of deconvolution parameters which will allow the software to preserve the isotopic resolution in uncharged spectrum. These are simply lowered values of m/z and Mass smoothing and spacing parameters. The following usually works well:
For extremely high resolution data, the user may lower the values further to avoid smoothing.
In order to direct Intact Mass to calculate the monoisotopic mass, the following advanced
parameter can be used:
This advanced command directs Intact Mass to compute monoisotopic masses and place them in the “Mass monoisotope” column in the Masses table. Intact Mass will compute monoisotopic masses for all the picked peaks, but it will use two different algorithms to do so. For masses up to 30000 (the value of the MaxMonoisotope parameter), Intact Mass will assume that the mass peaks are isotope-resolved, and match averagine isotope peaks to observed peaks. For masses greater than 30000, Intact Mass will assume that the mass peaks are not isotope-resolved, and it will simply subtract a correction factor from the observed average mass. The correction factor is the difference between the average isotope mass and monoisotopic mass for averagine. It’s worth noting that the MS1 colored dot is set to the tallest point within 0.6 / charge. This prevents a colored dot derived from the average neutral mass from falling between isotope-resolved m/z peaks.