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(3)CHO (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 (RCH(3)) or serine (RH) 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.