Journal
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
Volume 32, Issue 6, Pages 1278-1294Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jasms.1c00099
Keywords
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Funding
- National Institutes of Health (NIH) [R01 HL096971, R01 HL109810, R01 GM117058, R01 GM125085, S10 OD018475]
- Training Program in Translational Cardiovascular Science [T32 HL007936-20, T32 HL007936-19]
- American Heart Association [832615]
- Vascular Surgery Research Training Program grant [T32HL110853]
- Biemann Medal Award
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Top-down proteomics is a powerful technology for comprehensively characterizing proteoforms and understanding protein functions, disease mechanisms, and biomarkers. However, challenges in protein solubility, data analysis, and proteome complexity remain. Recent technological developments include the development of new surfactants, nanoparticles for enriching proteoforms, and strategies for multi-dimensional chromatography separation of proteins.
Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, induding the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.
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