How do I get the error for a deconvolution
There are several ways to report the error. The best is to run three experiments, measure the mass for each, and then take the standard deviation. That method will capture more of the experimental uncertainty, especially between needles.
If you want some other metrics from a single spectrum, you can right click any peak in the peak list panel and click “Centroid and Uncertainty”. That will give you both the FWHM of each peak, which is measured from the deconvolved mass. It will also give the Mean Error, which the standard deviation of the apex mass measured from different m/z values weighted by the intensity of the peaks. Basically, this metric assigns the charge states, calculates the mass for the peak m/z value, and then calculates the standard deviation based on the charge state distribution.
Overall, our recommendation is to do multiple experiments.