Challenges in label-free single-cell proteomics

This presentation by Marcel Bühler focuses on the implementation and challenges of single-cell proteomics at the VIB Centre for Medical Biotechnology. It highlights the significant increase in single-cell proteomics research and the importance of dedicated infrastructure and advanced instrumentation for success. 

The presentation discusses the optimization of sample preparation and LC methods, emphasizing the need for precise handling to avoid technical variations and ensure reproducibility. It also covers the use of μPAC™ columns to boost sensitivity and the importance of considering cell size effects in quantitative modeling. Marcel shares insights from various experiments, including the challenges faced with evaporation during sample prep and the solutions developed to mitigate these issues. 

The presentation concludes with a discussion on the potential of single-cell proteomics to provide meaningful data even with lower-tier instruments, given proper sample preparation and equipment mastery. 

Learning points :

• Infrastructure and Instrumentation: Success in single-cell proteomics requires dedicated infrastructure, advanced instrumentation, and sometimes even DIY equipment. Proper funding and early access to technology can significantly enhance research capabilities. 
• Sample Preparation and LC Methods: Optimizing sample preparation and liquid chromatography (LC) methods is crucial to avoid technical variations and ensure reproducibility. Techniques like using μPAC™ columns can boost sensitivity and improve method efficiency. 
• Quantitative Modelling and Data Handling: It's essential to consider cell size effects in quantitative modelling and rethink data handling strategies. Proper sample preparation, good reagents, and mastering equipment can yield meaningful single-cell proteomics data even with lower-tier instruments. 

Who should attend?

• Proteomics Researchers and Technicians: Individuals working in proteomics, especially those interested in single-cell proteomics, will benefit from insights into advanced instrumentation, sample preparation, and data handling techniques. 
• Biotechnology and Life Sciences Professionals: Professionals involved in biotechnology and life sciences who are looking to implement or optimize single-cell proteomics in their research will find valuable information on overcoming technical challenges and improving reproducibility. 
• Laboratory Managers and Funding Agencies: Those responsible for managing laboratory resources and securing funding will gain an understanding of the infrastructure and financial investments required for successful single-cell proteomics research. 

Presenter:  Dr. Marcel Bühler (Project Manager, VIB-UGent Center for Medical Biotechnology)

Dr. Bühler earned a PhD in Cancer Biology from the University of Zurich in January 2023, with a dissertation titled "Longitudinal Characterization of the Glioblastoma Proteome Using PCT-SWATH Mass Spectrometry." Prior to this, Marcelcompleted a Master of Science in Biology, majoring in Biochemistry, at the Swiss Federal Institute of Technology (ETH) Zurich in December 2018. Their master's thesis focused on "Characterization of Epigenetic Inhibitors by Complementary Phenotypic Analysis and Histone Epi-Proteomics." Marcel also holds a Bachelor of Science in Biology from ETH Zurich, obtained in September 2016.