Effects of Modified Digestion Schemes on the Identification of Proteins from Complex Mixtures

Abstract

In shotgun proteomics, a complex protein mixture is digested to peptides, separated, and identified by microcapillary liquid chromatography coupled with tandem mass spectrometry (LC−MS/MS). In this technology, complete protein digestion is often assumed. We show that, to the contrary, modifications to a standard digestion protocol demonstrate large, reproducible improvements in protein identification, a result consistent with digestion being a limiting factor in the efficiency of protein identification. Keywords: mass spectrometry • proteomics • digestion • protein identificatio