An overview of technologies for MS-based proteomics-centric multi-omics

Apr 25, 2022Expert review of proteomics

Overview of Technologies for Mass Spectrometry-Based Protein and Multi-Omics Analysis

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Abstract

Mass spectrometry-based technologies have improved the quantitative characterization of complex proteomes.

Proteomics provides a single level of molecular information but can be enhanced by integrating data from the genome, epigenome, transcriptome, and metabolome.
Advancements in peptide-based, bottom-up mass spectrometry techniques are enabling deeper analysis of proteomes.
The integration of proteomics data with other 'omic information offers a more comprehensive understanding of biological systems.
Current bioinformatics tools are essential for combining proteomics with other 'omics data to facilitate new discoveries.
Multi-omic approaches show potential for advancing biological and biomedical research.

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INTRODUCTION: Mass spectrometry-based proteomics reveals dynamic molecular signatures underlying phenotypes reflecting normal and perturbed conditions in living systems. Although valuable on its own, the proteome has only one level of moleclar information, with the genome, epigenome, transcriptome, and metabolome, all providing complementary information. Multi-omic analysis integrating information from one or more of these other domains with proteomic information provides a more complete picture of molecular contributors to dynamic biological systems.

AREAS COVERED: Here, we discuss the improvements to mass spectrometry-based technologies, focused on peptide-based, bottom-up approaches that have enabled deep, quantitative characterization of complex proteomes. These advances are facilitating the integration of proteomics data with other 'omic information, providing a more complete picture of living systems. We also describe the current state of bioinformatics software and approaches for integrating proteomics and other 'omics data, critical for enabling new discoveries driven by multi-omics.

EXPERT COMMENTARY: Multi-omics, centered on the integration of proteomics information with other 'omic information, has tremendous promise for biological and biomedical studies. Continued advances in approaches for generating deep, reliable proteomic data and bioinformatics tools aimed at integrating data across 'omic domains will ensure the discoveries offered by these multi-omic studies continue to increase.

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