The Prediction of the Ion Fraction of the Peptide with Selected Charge in Mass Spectrometry with Positive Electrospray Ionization

Abstract

The possibility of prediction of selected ion fraction in the total peptide fraction obtained during mass spectrometry with positive ionization by electrospray was investigated on the basis of the amino acid sequence. The data obtained in the MS / MS experiment [Ramus et al., 2015] using the standardized UPS1 kit (48 highly purified human proteins) and deposited in ProteomeXchange (identifier PXD001819) were used as the initial data set. For each of the identified peptides belonging to one of the proteins of the UPS kit, a list of detected ions of different charge was formed. The sum of the peak intensities detected for the primary ion was used as a measure of quantity. Since the ratio of the peptide fractions of ions with different charges does not depend on the concentration in the experimental sample, the total sample was assembled by combining the data obtained for different dilutions of UPS1. A set of equations of prediction of the fraction of 1+, 2+, and 3+ ions has been constructed. This computational analysis has shown applicability of the proposed for prediction of the ion fraction of the peptide with selected charge in mass spectrometry with positive electrospray ionization.