A mass spectrometry data processing apparatus includes a computation unit and a seeking unit. The computation unit calculates the mass difference Δm/z between the peaks of two molecules selected from mass spectrum data or obtains the mass difference Δm/z. The seeking unit estimates a combination of atoms between the peaks of the two molecules in a range of the mass difference Δm/z. The seeking unit seeks the combination of atoms having a mass difference, which matches the mass difference Δm/z, between a set of atoms desorbed from a first molecule of the two molecules and a set of atoms added to the first molecule.