Proteomics Tracing the Footsteps of Infectious Disease

Abstract

Every year, a major cause of human disease and death worldwide is infection with the various pathogens-viruses, bacteria, fungi, and protozoa-that are intrinsic to our ecosystem. In efforts to control the prevalence of infectious disease and develop improved therapies, the scientific community has focused on building a molecular picture of pathogen infection and spread. These studies have been aimed at defining the cellular mechanisms that allow pathogen entry into hosts cells, their replication and transmission, as well as the core mechanisms of host defense against pathogens. The past two decades have demonstrated the valuable implementation of proteomic methods in all these areas of infectious disease research. Here, we provide a perspective on the contributions of mass spectrometry and other proteomics approaches to understanding the molecular details of pathogen infection. Specifically, we highlight methods used for defining the composition of viral and bacterial pathogens and the dynamic interaction with their hosts in space and time. We discuss the promise of MS-based proteomics in supporting the development of diagnostics and therapies, and the growing need for multiomics strategies for gaining a systems view of pathogen infection. Molecular & Cellular Proteomics 16: 10.1074/ mcp.O116.066001, S5-S14, 2017.

Glycomics and Proteomics Approaches to Investigate Early Adenovirus–Host Cell Interactions

“…In addition to the development of glycan array technologies, the field of virology has in the past decade benefited from advances in mass spectrometry-based proteomics. In particular shotgun proteomics, which is the unbiased detection of all proteins in a given biological sample, holds great promise for the identification of host factors of viral infection [132][133][134]. The basic principle of shotgun proteomics is the digestion of all proteins in a mixture with a defined enzyme such as trypsin and the subsequent identification of proteins based on their characteristic peptide fingerprint, for example, tryptic peptides unique to one protein in the whole proteomic space of a given species.…”

Quantitative proteomic analyses in blood: A window to human health and disease

“…The potential clinical application of these novel biomarkers was further validated with ELISA . A number of proteomics approaches have been used to study the disease process of infection, to understand the molecular mechanisms of infectious disease during viral infection . The MS platform has been used to investigate bacterial responses under various environmental conditions and to define the infectious viral particle composition as well as mechanisms of viral replication and maturation and host cellular defense .…”

“…73 A number of proteomics approaches have been used to study the disease process of infection, to understand the molecular mechanisms of infectious disease during viral infection. [74][75][76] The MS platform has been used to investigate bacterial responses under various environmental conditions 77,78 and to define the infectious viral particle composition [79][80][81] as well as mechanisms of viral replication and maturation 82,83 and host cellular defense. 84 In one particular study, Machen et al used a combined lysis-filtration method with MALDI-TOF VITEK MS and the VITEK2 system to make a same day identification and full panel antimicrobial susceptibility testing of bacteria from positive blood culture bottles.…”

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission

“…Recent improvements in the sensitivity and accuracy of mass spectrometry have allowed for almost complete proteomic mapping of the human proteome, including that of fluids, cells, and tissues . Quantitative proteomics is increasingly being used to study infectious diseases, and improve our understanding of the pathogenesis of HIV, influenza, Chlamydia, and other infectious diseases . Post‐translational modifications (PTMs) can also be studied, such as phosphorylation, alkylation, glycosylation, and others, which are important for mucosal health including signal transduction, innate and acquired immunity, and physical barrier function .…”