Spectrum deisotoping based on the theoretical isotope intensity ratios by Valkenborg et al. (2008).

First, sequences of peaks at isotopic mass differences are identified. Next, the intensity ratios are compared to the expected theoretical intensity ratios based on the polynomial model by Valkenborg et al. A X² test is used to determine whether the ratios are similar enough.

@Valkenborg, a few questions if you don't mind.

• Could you have a look at the code to see if it correctly applies the procedure that you've described in your paper?
• Do you have an intuition about the threshold for the X² test? The manuscript says it depends on the data, which makes sense, but a robust default value would be useful. What's an appropriate magnitude for example?
• This research is more than a decade old by now, would you say that this is still the recommended way to deisotope MS2 spectra?