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Extraordinary science with Ben Garcia

At the Washington University School of Medicine in St. Louis, Benjamin Garcia focuses on epigenetics by leveraging the latest mass spectrometry technologies to study post-translational and post-transcriptional modifications.

Unveiling epigenetic modifications and their significant impact on health and diseases

Epigenetics play a crucial role in human health and disease. Epigenetics is the study of complex molecular interactions that cause transmissible modifications to gene activity, but without altering the DNA sequence itself. The regulation of epigenetics involves several key mechanisms, including DNA methylation, histone modification, and RNA-mediated processes. Ultimately, epigenetic modifications effect how the body interprets DNA sequences thus playing a crucial role in both normal human physiology and the pathogenesis of various diseases. For example, the dysregulation of epigenetic mechanisms has been linked to a wide range of conditions, such as cancer, cardiovascular diseases, neurological disorders, and more. Fortunately, unlike genetic mutations, epigenetic modifications are reversible enabling epigenetic therapies to be an exciting development in medicine. Drugs targeting DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) are already in clinical use for certain cancers. [1]

Traditionally, chromatin biologists have studied histone modifications one at a time due to the limitation of reagents available to them. However, histone proteins are subject to over 100 different types of post-translational modifications, which can also influence each other. To address this complexity, analytical chemists are increasingly turning to mass spectrometry (MS). By using MS, multiple modifications can be simultaneously identified in a single analysis offering comprehensive insight to the sample of interest. Continued research in this field encourages the potential of novel diagnostic tools and therapeutic strategies that can transform the approach towards a wide range of medical conditions. 

[1] Chakrabarti SK, Chattopadhyay D. (2024) Expanding Role of Epigenetics in Human Health and Disease. Explor Res Hypothesis Med. Published online: Jan 11, 2024. doi: 10.14218/ERHM.2023.00086.

Key takeaways

  • The ZenoTOF 7600 system offers leading edge technology for the characterization of many labile and non-labile protein and RNA modifications.
  • The speed of the ZenoTOF 7600 system enabled the laboratory to develop a very fast, 10-minute high-throughput SWATH method for histone PTM analysis (using bottom-up mass spectrometry).
  • Electron activated dissociation (EAD) enables in-depth and complementary bottom-up and top-down analysis of histones.
  • Rich EAD MS/MS spectra were extremely useful for mapping combinations of epigenetic modifications. The results identified the precise location and novel combinations of modification.
High energies rendered by tunable EAD identified two different modifications on co-eluting peptides that would otherwise be undistinguishable using standard fragmentation capabilities. The spectrum on the left presents an acetyl and methyl group found together on the same lysine group, whereas the spectrum on the right indicates a proprionyl group on the lysine. This is the first evidence of having an acetyl and methyl group found on the same lysine residue in biology.

    • "We have decided to make a very high throughput analysis for these histone proteins that carry all these different modifications. Typically, our gold standard approach was to use an hour and a half gradient using nanoflow, liquid chromatography feature on various different types of high-resolution instruments. But we thought, can we shrink that down to a ten-minute run?"

      Ben Garcia Head of Biochemistry and Molecular Biophysics Washington University in St. Louis

    Watch Ben Garcia's extraordinary science

    Enhancing epigenetic modification analysis using LC-MS/MS

    About the presenter


    Prof. Dr. Benjamin Garcia

    Ben Garcia is a Raymond H. Wittcoff Distinguished Professor, head of the Department of Biochemistry and Molecular Biophysics, and a preeminent authority on the proteomics of epigenetic regulation. A recognized leader in mass spectrometry, he has made seminal contributions to understanding histone biology and its role in physiologic and pathophysiologic processes. Recognized with many awards including the American Society for Mass Spectrometry Biemann Medal, Dr. Garcia is at the forefront of academic and industry approaches to quantitative proteomics. Diabetes and its metabolic consequences are known to have robust effects on metabolic modifications of proteins implicated in disease progression. Dr. Garcia is interested in contributing to the reorganized DRC Mass Spectrometry Core directed by Dr. Ben Major to leverage an institutional omics commitment to identify mechanisms underlying diabetes and its complications.

    The fundamentals behind extraordinary science

    Zeno trap
    The innovation of the Zeno trap solves the duty cycle issue observed on other QTOF instruments. As ions are accumulated in the Zeno trap before being pulsed rapidly into the TOF, up to 20x more fragment ions can be detected. Each TOF experiment therefore acquires more useful MS/MS information, including for lower abundance species that were previously undetectable. The use of the Zeno trap introduces researchers to a new level of sensitivity.
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    Zeno SWATH DIA
    Zeno SWATH data-independent acquisition (DIA) combines the sensitivity of the Zeno trap with the reproducibility and precision of SWATH DIA to deliver unprecedented levels of analyte identification and quantitation. The 6–10x sensitivity gains in MS/MS mode that the Zeno trap provides through duty cycle improvements deliver up to 3x more identified proteins and approximately 3–6x more quantified proteins at loads less than 20 ng. This leads to a more comprehensive understanding of underlying biological changes. With Zeno SWATH DIA, maximal information is obtained from each precious sample.
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    Electron associated dissociation (EAD)
    EAD is a step-change in fragmentation technology that allows for a range of free electron-based fragmentation mechanisms within 1 device. The ability to tune electron kinetic energy within an EAD experiment extends the utility of the approach to all molecule types, ranging from singly charged small molecules to large multiply charged proteins.
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