Introduction

Studying Signal-transduction Pathways using Targeted Proteomic Workflows

Our laboratory uses quantitative mass spectrometry as a platform to delineate signaling networks in normal and diseased biological systems. Current mass spectrometry-based proteomic workflows focus on sequencing every gas-phase peptide ion present in a complex biological sample using data-dependent tandem mass spectrometry. This approach, which is commonly referred to as “shotgun proteomics”, is the primary workflow for interrogating low- and high-complexity protein samples. However, recent software advances in the acquisition, control, and processing of MS spectra on high-resolution mass spectrometry instruments have catalyzed the birth and evolution of targeted mass spectrometry (targeted MS)-based proteomic strategies. Targeted MS, also known as directed MS, offers a robust and superior reverse proteomic strategy for pre-selecting and targeting gas-phase peptide ions for tandem MS sequencing. Targeted MS workflows facilitate the detection and quantification of low-abundance peptide ions in complex protein mixtures, an approach that is conceptually identical to picking a needle out of a haystack. In contrast, shotgun proteomic approaches, whose goal is to exhaustively sequence all gas-phase peptide ions in the sample of interest, lack the power to reproducibly detect low-abundance peptide ions of interest in complex biological samples. Targeted MS strategies will thus provide new opportunities for identifying, quantifying, and monitoring the dynamic actions of protein networks in complex biological systems. We expect targeted proteomics to transform biological and biomedical research in the foreseeable future.