Horizontal Integration: OMICS – Mass Spectrometry-Based Proteomics in Systems Biology Research

Abstract

Mass spectrometry-based proteomics has already contributed greatly to systems biology studies and its role in systems biology research is likely to grow in the next few years. Its unique capability of quantifying proteins and protein modifications at large scale and throughput make it a prime technology in systems biology studies, specifically those focused on complex biological processes and diseases. In this article, we first introduce the motivation and challenges of using proteomics in systems biology studies. Second, we give an overview of the most common methods to measure and quantify proteins using liquid-chromatography coupled tandem mass spectrometry. In the third section, we highlight how mass spectrometry contributes to generating functionally highly relevant proteomic information that goes beyond the identity and quantity of constituent proteins (i.e., mapping the proteoforms, mapping the interactions, and relating the proteome to the genome), and then we focus on three exemplary biological processes to show how mass spectrometry-based studies contributed to increasing our understanding of them.