Abstract. A database of 1470 collision cross sections (666 doubly-and 804 triplycharged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M 2+ ) correspond to Mg 2+ , Ca 2+ , or Ba 2+ ] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M 2+ -coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M 2+ -coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M 2+ binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition
