High-throughput proteomics: a methodological mini-review

Abstract

Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other ‘omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.

Mass Spectrometry-Based Proteomics of Minor Species in the Bulk: Questions to Raise with Respect to the Untargeted Analysis of Viral Proteins in Human Tissue

“…Moreover, comprehensive protein sequence databases are not available for every species of potential interest, resulting in a bias in the search results towards known proteins. Database quality, instrumentation, and data processing tools are, however, constantly improving at lowering the limit of detection further [ 2 , 3 , 4 ]. Nevertheless, it will still be necessary to evaluate proteomics results according to the principles of analytical chemistry.…”

“…MS has been a driving force in proteomic analysis for more than 20 years and still is, despite the fact that, increasingly, complementary technologies are being introduced to the market. These include antibody- and aptamer-based assays, as well as proximity extension assays (for reviews on technical advances in proteomics, see [ 2 , 3 ]). MS-based experiments rely on high-resolution/high-mass accuracy instrumentation.…”

Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance

“…Advances in proteomics will help in elucidating how the yield and nutrient content are affected by adverse conditions such as stress resulting from drought [ 19 ]. Proteomics, one of the key tools of the post-genomic era [ 20 ], offers sensitive identification of the proteins associated with drought responses in plants [ 21 , 22 , 23 , 24 ].…”

Expanding Glycomic Investigations through Thiol-Derivatized Glycans

“…In contrast, the field of proteomics has brought about innovative [ 8 ], selective, mild [ 9 ], and occasionally reversible modifications [ 10 ] of proteins enabling site-specific tagging [ 11 ] and pull-down approaches [ 12 ]. Therefore, the field of proteomics has rapidly progressed with assigning structures and functions to an ever-increasing number of targets [ 13 ]. Many of these chemical biology approaches exploit thiol chemistry, including intrinsically present cysteine residues, due to the soft nucleophilic nature of thiol groups [ 14 , 15 , 16 ].…”