Optimizing Peptide Selection for Quantitative Proteomics: A Mixed Method Approach to Enhance Accuracy and Precision

Simon Perrin, Jean-François Noël, Jean-Claude Chartrand, Hugo Gagnon

Allumiqs, Sherbrooke, QC, Canada

Introduction

Traditional benchmarking often prioritizes proteome coverage, aiming to maximize peptide and protein identifications, while quantification accuracy receives limited focus. The industrial gold standard is the Top5 approach where protein intensities are inferred by the summed intensity of their 5 most intense peptides. Signal saturation may lead to impaired linear signal-concentration response at high concentration.