Targeted histidine-peptide enrichment improved the accuracy of isobaric-based quantitative proteomics

Abstract

Liquid chromatography combined with tandem mass spectrometry has been widely used for in-depth proteome profiling and to quantitatively measure proteome regulation. However, due to peak capacity constraints, differences in peptide properties and other factors in total proteome analysis, only limited protein sequence coverage can be obtained. A large number of co-eluted peptides may act as a matrix and co-fragment with the targeted parent ions, seriously affecting the accuracy of fragment ion-based quantitative proteomic analysis. To simplify the complicated peptide mixture and improve the accuracy of the quantitative mass spectrometric analysis, this research explored a method for selective enrichment of peptides containing histidine (his-peptides). The experimental conditions, including Cu-bead preparation, the binding duration of his-peptides to the beads, and the ratio of the total peptide mass to volume of the beads, were evaluated. The optimized procedure for his-peptide enrichment was fast and robust and provided 70% recovery of the his-peptides in a highly reproducible way. When combined with an exemplary iTRAQ experiment, the his-peptide enrichment approach can significantly improve the accuracy of the quantitative analysis. Therefore, his-peptide enrichment can be used as a simple, effective strategy to simplify the complex proteome and improve the accuracy of quantitative proteome research.