Ions near the high-end border of a mass defect distribution plot for native peptide fragment ions have potential as signature markers that are based on mass-to-charge ratio determination. The specificity of these marker ions, including phosphoryl ions, can be improved by removing interfering isobaric ions from the border region on the distribution plot. These interfering ions are rich in Asp and Glu content. The masses of amino acid residues and peptides are rescaled from the IUPAC scale (12C = 12 u as the mass reference) to the averagine scale (averagine mass = 111 u* as the mass reference with zero mass defect; u*: the mass unit on the averagine scale), using a scaling factor of 0.999493894. It is theoretically predicted that esterification of Asp and Glu side-chain carboxylates with n-butanol can achieve a sufficient retreat of the high-end border on a mass defect distribution plot based on the use of mass spectrometers with better-than-medium resolution. Theoretical calculations and laboratory experiments are performed to examine effects of various esterifications on the averagine-scale mass defect distribution of peptide fragment ions and on the specificity of two positive phosphoryl ions: the phosphotyrosine immonium ion and a cyclophosphoramidate ion.