High-throughput microdroplet-based analysis of post-translational protein modifications using mass spectrometry

Abstract

We present a novel microdroplet-based microarray interface between nano-LC and MALDI-MS and demonstrate its versatility for the reliable identification of post-translational protein modifications. A tryptic protein digest containing phosphorylated and glycosylated peptides is separated by a standard nano-LC run, the eluate is compartmentalized into microdroplets and spotted onto a microarray plate, thereby conserving the chromatographic separation. A single eluting peak is split over multiple sample spots. Specific enzymes are applied to every second sample spot to remove the modification, which results in a mass shift for modified peptides. Due to this, a comparison between two consecutive MS spectra allows a robust identification of peptides carrying post-translational modifications.