A database of alkali metal-containing peptide cross sections: Influence of metals on size parameters for specific amino acids

Ion mobility/mass spectrometry techniques have been used to generate a cross section database containing 1772 entries (147 singly-, 1325 doubly-, and 300 triply-charged) for protonated and alkalated tryptic peptide ions. Such a large number of values make it possible to assess the influence of alkali metal cations [where the cation (M.) corresponds to Lit, Na+, K+, or Cs+] on peptide ion conformation. Peptide ion sizes generally increase with increasing cation size relative to the respective singly- or doubly-protonated species. Intrinsic size parameters for individual amino acid residues for alkali [Pep+M+H](2+) and [Pep+2M](2+) ions are similar to those obtained from the [Pep+2H](2+) ions. However, polar residues (Asp, Glu. Asn, Gln, His, and carboxyamidomethylated Cys), as well as Met, appear to be substantially smaller for metal-containing [Pep+M+H](2+) species compared with [Pep+2H](2+) species. This suggests these residues form tight binding interactions with these metals. A discussion of these results and the implications regarding structure are provided. (C) 2012 Published by Elsevier B.V.