How does mass spectrometry detect histone methylation?
It is not simple MS, it is tandem MS. They send the sample through multiple MS and they fragment it between them. So they can get info about the molecular structure as well, not just the mass/charge of the molecule.

A quote from your article:


  MS/MS spectra of the methylated H3 protein (top down) and fragments
  upon electron transfer dissociation fragmentation. Fragments of the
  methylated H3 have a mass shift of 42 starting at C14, indicating a
  modification site at the K14 at the N terminus of the peptide.
  Normalized collision energy = 35%, activation Q = 0.250, activation
  time = 100 ms, accumulation time = 5 min.


A reference from your article:


  Frese et al., 2011 C.K. Frese, A.F. Altelaar, M.L. Hennrich, D.
  Nolting, M. Zeller, J. Griep-Raming, A.J. Heck, S. Mohammed
  
  Improved peptide identification by targeted fragmentation using CID,
  HCD and ETD on an LTQ-Orbitrap Velos
  
  J. Proteome Res., 10 (2011), pp. 2377–2388