Study of factors governing negative molecular ion yields of amino acid and peptide in FAB, MALDI and ESI mass spectrometry

The factors governing negative and/or positive molecular ion yields of amino acids and peptides in the soft ionization methods of fast atom bombardment (FAB), matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry have been examined. The results obtained have been interpreted from the standpoint of two different components, namely desorption and ionization, by relating the ion yields to physicochemical properties of amino acid and peptides. The negative-ion yields of amino acids in FAB were found to be dependent on gas-phase acidity and aliphatic/hydrophobicity. In MALDI, a linear correlation was observed between negative-ion yields and gas-phase acidity of amino acids. In both FAB and MALDI mass spectra of peptides, the presence of aspartic acid residues tended to enhance the negative-ion yields. The presence of aliphatic/hydrophobic residues in FAB or aromatic amino acid residues in MALDI enhanced the negative-ion yields of peptides. In ESI, the charge state distributions of multiply-protonated peptides were dependent on the number of basic sites and their position in the sequence, while those of multiply-deprotonated peptides were dependent on the number of acidic sites. The total ion yields in ESI were governed by hydrophobicity of peptides and efficiency of acquiring the charge(s). The results suggest that the ion yields were governed by two independent processes, namely ionization and desorption, regardless of the ionization methods used.