Extraordinary science with Hugo Gagnon

At Allumiqs, Hugo Gagnon investigates high-throughput proteomics to validate new drug development

  • “It's important to use a system that gives you great signal-to-noise and a good sensitivity to have deep proteome coverage. That's what Zeno SWATH DIA on the ZenoTOF 7600 system provides you and it's very important if you think about a larger study design.”

    Hugo Gagnon Chief Scientific Officer Allumiqs

Exploring high-throughput proteomics for new drug development

The amazing complexity of cellular networks is still not fully understood and therefore modifying a single gene to treat a patient can have various effects that need to be determined. Answering the questions about what is happening at the cellular level requires an untargeted and very sensitive approach. State-of-the-art, highly sensitive Zeno SWATH data-independent acquisition (DIA) can determine off- and on-target effects with unprecedented depth and short injection-to-injection times that allow for necessary throughput. Here, Hugo Gagnon will discuss experimental design, depth of analysis, target coverage and statistical challenges to help biopharmaceutical drug developers ensure safe and efficient gene therapy products.

Key takeaways

  • Using LC-MS based proteomics for high-throughput drug discovery is feasible
  • High-throughput proteomics offers an in-depth, unbiased approach to overcome the limitations of common methods for drug development (for example, PROTACs and CRISPR)
  • High-throughput proteomics requires careful project design for optimization
  • Depth of coverage vs. acquisition speed
  • Robustness vs. study design
  • Technical variability (instrument, biological, processing)
  • Faster gradients can be beneficial beyond their use for high-throughput proteomics by supporting better chromatography with sharper and taller peaks with improved signal-to-noise ratio

Watch Hugo Gagnon’s extraordinary science

High-throughput proteomics in drug development with Zeno SWATH DIA for PROTAC screening and CRISPR validation applications

About the presenter

Hugo Gagnon, PhD
Chief Scientific Officer

Hugo Gagnon is the Chief Scientific Officer of Allumiqs. Previously, he served as the CEO and co-founder of PhenoSwitch Bioscience, which was acquired by Proteoform Scientific to create Allumiqs in 2022.

During his PhD, Hugo used mass spectrometry through different collaborations and core facility services to answer biological questions. He quickly learned that access to mass spectrometry necessitates a considerable resource investment to obtain desirable results. Thus, PhenoSwitch Bioscience was founded with a team of expert scientists to address this need. Hugo studied at Université de Sherbrooke, where he earned a BSc in biochemistry, MSc in pharmacology and a PhD in biochemistry. Hugo has been the driving force behind the innovative LC-MS/MS services offerings tailored with deep data analytics insights and the high-quality reputation the company has developed within the biotech, omics, and mass spectrometry industries. Through the years, Hugo has developed deep expertise in LC-MS/MS-based omics, protein science and data science for omics analysis.

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.
Read more
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.
Read more
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.
Read more