In this paper, we present a probabilistic CNL model that only requires information from the mass domain for the deconvolution of fragment ions for small molecules (<1000 Da). The performance of the CNL model was evaluated for both fragments from spectral databases (i.e. MassBank EU and MassBank of North America) and measurements containing predominantly pesticide standards. The latter were also evaluated at different sample concentrations and with varying levels of added background matrix. Moreover, the model performance was compared with two frequently used methods, including peak apex retention time difference and peak shape correlation.