Here’s some general information about my current projects in the MacCoss lab. Feel free to reach out if you have any questions!
- Extracellular vesicle isolation from biofluids
- Extracting conserved proteomic aging biomarkers
- Quality control in quantitative mass spectrometry
Extracellular vesicle isolation from biofluids
Extracellular vesicles (EVs) are membrane-bound particles that carry critical biological cargo. If you think of our blood as a physiological highway, moving signalling molecules throughout the body between organ systems, then EVs are highly sophisticated delivery vehicles. In terms of mass spectrometry, they also contain the most biologically significant proteins typically measured in blood. This approach let’s us get a better picture of the state of an organism.
The MacCoss lab has developed a novel technique to isolate EVs from plasma, the liquid portion of blood, quickly and robustly called Mag-Net. A preprint is now available on bioRxiv that summarizes the method. Please reach out with any questions!
Relevant GitHub Repository: uw-maccosslab/Mag-Net
Wu CC, Tsantilas KA, et al. (2023). Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv
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Extracting conserved proteomic aging biomarkers
Collaborators: The Dog Aging Project and Dr. Gary Churchill’s Laboratory at the Jackson Laboratory.
The biology of aging frequently relies on model organisms to further our understanding of fundamental processes. As interspecies studies have become more frequent, the need for tools and approaches tailored to each species has become crucial. I’m working to develop a series of data-independent acquisition mass spectrometry assays to measure proteins in plasma extracellular vesicles (EVs) in humans, laboratory mice, and companion dogs.
Biologically, I’m interested in how the composition of the EV proteome changes with age within each species, and what changes are conserved across the lifespan of all 3 species.
I’m currently analyzing the mouse dataset in this project and have seen exciting results already that I can’t wait to share!
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Quality control in quantitative mass spectrometry
Mass spectrometry is a sensitive and powerful tool to characterize the proteome. Despite best practices and intentions, issues happen! The MacCoss lab developed an adaptable framework to identify problems in an experiment, pinpoint their origin, and determine changes that need to be made.
We use three classes of quality controls: system suitability, internal quality controls, and external quality control samples. All serve as “checkpoints” for evaluation of an experiment, although they differ in composition, preparation, and the stage they are introduced into a workflow.
System suitability are targeted runs of known quantities of peptide standards run prior to, interspersed with, and after experimental samples. They are tracked longitudinally regardless of the instrument operator and experiment. Internal QCs are added to individual samples to monitor sample processing. External QC samples include the same internal QCs added to experimental samples, but these samples are prepared multiple times in an experiment (Or in multiple experiments) assess sample preparation variability, signal processing, and normalization.
The application of this framework in real-world experimental vignettes has just been published in the Journal of Proteome Research. Please reach out with any questions!
Relevant GitHub Repository: uw-maccosslab/maccoss-sample-qc-system-suitability
Tsantilas KA, et al. (2024). A Framework for Quality Control in Quantitative Proteomics. Journal of Proteome Research
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