Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

Abstract

Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein–protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.

Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics

“…Proximity labeling methods (right) require a plasmid construct with the protein of interest fused to a proximity labeling enzyme, which after expression can be combined with biotin to covalently modify all nearby proteins for streptavidin enrichment. This figure was originally published by Pino et al Biochem Soc Trans 30 October 2020; 48 (5): 1953-1966 [18].…”

Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments

“…Mass spectrometry-based proteomics is a broad term encompassing many applications 6 used across different biological systems 7 , and accordingly has an abundance of software tools available 8 . Protein inference is made possible by peptide identification following database searching of tandem mass spectrometry data 9 .…”

“…The environment is accessed via any client with internet access (1). Data for analysis can be retrieved directly to the environment from private data sources (5) and public data repositories (6). Computational resources can be assigned to the environment prior to analysis (2), at which point programs (4) or workflows (3) may be used to complete the analysis.…”

Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review

“…The availability of the hybrid mass spectrometer with high sensitivity and mass accuracies such as hybrid linear trap orbitrap mass spectrometer, triple quadrupole mass spectrometer, quadrupole-orbitrap mass spectrometer, triple quadrupole/linear ion trap mass spectrometer, and orbitrap fusion tribrid mass spectrometer, has driven researchers to carry out label -based and label-free relative and absolute quantification of protein expression [ 111 – 113 ]. For label-based mass spectrometric approaches, stable isotope labelling by amino acids in cell culture (SILAC), isotope-coded affinity tag (ICAT), tandem mass tag (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ) are being used to spike the proteins from various biological samples to analyse and quantify the proteins through LC–MS/MS [ 114 ].…”