Li⁺ and Na⁺ attachment to some dipeptides via LDI-TOF mass spectrometry: Fragmentation patterns

Laser desorption ionization-time of flight (LDI-TOF) mass spectrometry is used for studying the attachment of Na⁺ and Li⁺ ions to four dipeptides including phenylalanyl-alanine (Phe-Ala), tyrosyl-alanine (Tyr-Ala), L-Phenylalanyl-L-Phenylalanine (Phe-Phe), and alanyl-glutamine (Ala-Gln) dipeptides. The LiCl, NaOH, and NaF salts are used as the source of Li⁺ and Na⁺ ions in the LDI of the dipeptides. Our aim is the investigation of the difference between the fragmentation patterns of the selected dipeptides in the presence of Na⁺ and Li⁺ ions due to the laser radiation and providing information for the fragmentation of larger peptides in the same conditions. The characteristic peak, related to [dipeptide-H + 2Na]⁺ species, is observed in the mass spectrum of Phe-Ala and Tyr-Ala dipeptides in the presence of NaF, while the breaking of the peptide bond (OC-NH) occurs for the Phe-Phe in the presence of the aforementioned salts. The characteristic peak of Ala-Gln dipeptide ([(Ala-Gln)-H + 2Na]⁺) is observed in the absence of any salt. The mass spectra of the dipeptides, recorded in the presence of LiCl, are crowded compared to those recorded in the presence of NaF and NaOH showing the effect of the type of alkali salt on the dipeptide fragmentation. The theoretical calculations are employed to investigate the ability of the interaction sites of dipeptides for the attachment of one and two Na⁺ and determine the most stable structure of the [dipeptide-H + 2Na]⁺ species for each dipeptide.