Next-generation proteomics: towards an integrative view of proteome dynamics

Key Points Our understanding of cellular function depends on exquisite knowledge of all of the molecular components acting in a system. Mass spectrometry (MS)-based proteomics has matured immensely in the last decade, allowing quantitative system-wide analysis of the proteome, including post-translational modifications (PTMs), protein–protein interactions and cellular localization. Quantification of the entire set of proteins expressed in a complex biological system (for example, mammalian cells) is now possible with a high sensitivity and in a reasonable amount of time. With the availability of genomic information, the massive capacity for peptide identification by MS is being used to annotate gene sequences and to find new protein-coding genes and splicing variants. In combination with new approaches to isolate specific PTMs, MS-based studies are revealing a much higher order of proteome complexity in which most proteins are modified by several PTMs that crosstalk in intricate mechanisms to regulate protein function. Protein affinity strategies allow purification of candidate proteins and their interacting partners, which are subsequently identified by MS. These studies describe, with a high degree of detail, dynamic and context-specific protein–protein interaction networks and protein complexes. The improvements in sensitivity, robustness and high-throughput of MS-based proteomics now permits applications in the clinical field, including the possibility of discovering disease-related biomarkers and screening molecular targets of candidate drugs. Despite their complexity and dynamics, proteomes are starting to be comprehensively characterized; this has been made possible particularly by various technical advances in mass spectrometry. This Review highlights how proteomic studies are contributing to our understanding of various cellular processes in health and disease. Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics