Multiplexed protein measurement: technologies and applications of protein and antibody arrays

Abstract

Multiplexed protein measurement is a rapidly advancing field that has the broadest potential to transform drug discovery and development in the next ten years of any existing 'omics' technology. Multiplexed protein measurement is logical for biological discovery with proteins because they function within networks, pathways, complexes and families. The activity of an individual protein is dependent not only on its abundance, but also on the effects of interacting proteins, modifying proteins, and antagonistic and synergistic proteins. However, until recently, specific, sensitive, multiplexed protein measurement has not been generally performed because of technical challenges, including the diverse physicochemical properties of proteins, their lability and interferences introduced as a by-product of multiplexed measurement reagents. Nevertheless, reports of discoveries made using multiplexed protein measurment technologies are starting to drive adoption of these approaches, and this article reviews these technologies, emerging standards, applications and remaining challenges. Four main applications that follow a logical research and development succession are discussed: surveys of changes in protein abundance; modelling networks, pathways, physiological and disease states; biomarker validation; and clinical diagnostics. The two principal types of technologies in use today in these applications are mass spectrometry and protein arrays, both of which discussed here, with a focus on protein arrays. Three broad categories of antibody microarray experimental formats are described: direct labelling, single-capture antibody experiments; dual antibody, sandwich immunoassays; and antigen or peptide capture arrays, with single read-out antibodies. Advantages and disadvantages of these formats are compared. The process of developing biomarkers based on multiplexed protein measurement into a clinical diagnostic test is discussed. The first step is multiplexed immunoassay development, in which optimized, multiplexed assays are developed for validated biomarkers and transferred to an immunodiagnostic platform. The second step is in vitro diagnostic development, driven by regulatory, manufacturing and marketing considerations.