Abstract: Provided is a method for processing data from a mass spectrum generated from a sample, which method comprises: (a) selecting a first peak in the mass spectrum; (b) selecting a first monoisotopic reference ion having a first charge state, which first reference ion could contribute to the first peak; (c) for one or more other isotopic forms of the first reference ion determining one or more further expected peaks in the mass spectrum; (d) comparing one or more of the determined further expected peaks with the mass spectrum to determine whether there are one or more peaks present in the spectrum that match the one or more determined further expected peaks; (e) if one or more of the determined further expected peaks match one or more of the peaks in the mass spectrum, designating the first peak as a data peak, and optionally designating the one or more peaks present in the spectrum that match the one or more determined further expected peaks as data peaks; (f) if the determined further expected peaks do not match