In a previous report J.W. de Beukelaar, J.W. Gratama, P.A. Sillevis Smitt, G.M. Verjans, J. Kraan, Th.M. Luider, P.C. Burgers, Rapid Commun. Mass Spectrom. 21 (2007) 1282 on the quality assessment of synthetic peptides used in protein-spanning peptide pools by matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) we noted that certain peptides showed remarkably intense signals for their calcium-containing analogues. Here we report on a detailed mass spectrometric study of the unimolecular chemistry of these calcium-containing peptides. By integration of the experimental findings with computational results derived from DFT and the CBS-QB3 model chemistry, we have traced the processes induced by Ca 2+ attachment in the peptide ions. Key to our analysis is the observation that all of the studied calcium-bound peptides containing a threonine or serine residue show prominent losses of CH 3CH O (from threonine) and/or CH 2 O (from serine) in both the positive and the negative ion mode. In the first step, Ca 2+ attaches itself to a negatively charged in-chain carboxylate group. Next, electrophilic attack of the calcium ion on the CH(R)OH group of threonine (R CH 3) or serine (R H) releases the hydroxyl proton which can then move to a suitable acceptor site, viz. a peptide bond. This leads to the formation of a very stable ionic bidentate structure. Upon collisional activation (MS/MS), this bidentate opens up leading to the loss of the exposed acetaldehyde or formaldehyde molecule, to yield another bidentate structure. MS/MS spectra of selected peptides interacting with other metal ions have also been investigated and it is found that only divalent ions follow the Ca 2+-induced transformations.