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In a high‐resolution MALDI‐TOF mass spectrum, a peptide produces multiple peaks, corresponding to the isotopic variants of the molecules. An overlap occurs when two peptides appear in the vicinity of the mass coordinate, resulting in the difficulty of quantifying the relative abundance and the exact masses of these peptides. To address the problem, two factors need to be considered: (1) the variability pertaining to the abundances of the isotopic variants (2) extra information content needed to supplement the information contained in data. We propose a Bayesian model for the incorporation of prior information. Such information exists, for example, for the distribution of the masses of peptides and the abundances of the isotopic variants. The model we develop allows for the correct estimation of the parameters of interest. The validity of the modeling approach is verified by a real‐life case study from a controlled mass …