Accuracy Requirements for Peptide Characterization by Monoisotopic Molecular Mass Measurements

Abstract

Accurately measured monoisotopic mass of a biomolecule can reveal its elemental and, in the case of a biopolymer, its monomer composition. In this work, the limitations of the technique were analyzed in application to peptides. For the currently available level of mass accuracy of about ±1 ppm, the mass limit for revealing the unique elemental composition of a peptide was found to be 700−800 Da, with the possibility to extend this range as the mass accuracy improves. As for the amino acid composition determination, the principal limit of ∼500−600 Da cannot be overcome in the general case by instrumental or methodological improvements. It is proposed that, for the peptide characterization, the molecular mass must be determined with sufficient accuracy to rule out a significant fraction of the peptides having the same nominal mass but different elemental and amino acid compositions. An accuracy of ±1 ppm was found to exclude 99% of such peptides and, therefore, ensure a high degree of confidence in peptide characterization.