Normalization of organ-on-a-chip samples for mass spectrometry based proteomics and metabolomics via dansylation-based assay

A discussion of the recently published paper, “Normalization of Organ-on-a-Chip Samples for Mass Spectrometry Based Proteomics and Metabolomics via Dansylation-based Assay,” and how the field can produce more replicable experiments.

About this webinar

Mass spectrometry based ‘omics pairs well with organ-on-a-chip-based investigations, which often have limited cellular material for sampling.  However, a common issue with these chip-based platforms is well-to-well or chip-to-chip variability in the proteome and metabolome due to factors such as plate edge effects, cellular asynchronization, effluent flow, and limited cell count. This causes high variability in the quantitative multi-omics analysis of samples, potentially masking true biological changes within the system. Solutions to this have been approached via data processing tools and post-acquisition normalization strategies such as constant median, constant sum, and overall signal normalization.

Unfortunately, these methods do not adequately correct for the large variations, resulting in a need for increased biological replicates. The methods in this work utilize a dansylation based assay with a subset of labeled metabolites that allow for pre-acquisition normalization to better correlate the biological perturbations that truly occur in chip-based platforms. BCA protein assays were performed in tandem with a proteomics pipeline to achieve pre-acquisition normalization. The CN Bio PhysioMimix was seeded with primary hepatocytes and challenged with VX after six days of culture, and the metabolome and proteome were analyzed using the described normalization methods. A decreased coefficient of variation percentage is achieved, significant changes are observed through the proteome and metabolome, and better classification of biological replicates acquired because of these strategies.

Key Takeaways

  • Learn about our recently published paper “Normalization of Organ-on-a-Chip Samples for Mass Spectrometry Based Proteomics and Metabolomics via Dansylation-based Assay”
  • Explore how we applied the danyslation normalization methods to the CNBio system to produce more robust metabolomics data
  • Cover how our lab is applying this normalization to CNBio and other microphysiolgical systems.

Our speaker

Erin Gallagher, PhD., CCDC Chemical Biological Center. US Army

Dr Erin Gallagher received her doctorate in 2019 from Johns Hopkins University, focusing on in vitro blood brain barrier models and nanoparticle delivery to the brain. She received a National Research Council postdoctoral associateship at the U.S. Army DEVCOM Chemical Biological Centre. Her postdoctoral work focused on developing and standing up microphysiological systems, including Emulate, CNBio, and TissUse. She has transitioned into a civilian position working on brain and blood brain barrier models, as well as continuing evaluating and using MPS systems for toxicological analysis.