Week 1 HW: Principles and Practices

Week 3: Lab Automation

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  1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

    Olsen J.V. et al. Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics (2024) Mol Cell Proteomics 23(7), 100790. DOI 10.1016/j.mcpro.2024.100790

This article describes a fully automated workflow for preparing clinical proteomics samples, from protein digestion to loading peptides into Evotips (disposable, tip-based C18 reversed-phase trap columns), ready for LC-MS/MS analysis. They use the Opentrons OT-2 liquid-handling robot, which controls all preparation steps without manual intervention after the initial loading of reagents. The process combines protein capture through aggregation on magnetic beads with enzymatic digestion and, without centrifugation steps, directly transfers the peptides to Evotips using positive pressure, all programmed through downloadable scripts from the Evosep website. Using this method, up to 192 samples can be processed in parallel in approximately 6 h, which equals to 100 samples/day and eliminates human variability. In tests with HeLa lysates, the workflow identified ~8.000 protein groups and ~130.000 peptides using an 11.5-min gradient on the Orbitrap Astral, demonstrating high sensitivity and reproducibility. It was also applied to 192 plasma samples from patients with metastatic melanoma, revealing clinically relevant protein changes.

  1. Write a description about what you intend to do with automation tools for your final project.

For my final project, I want to design a nanobiosensor using metallic nanoparticles (such as gold or silver, maybe (if possible) carbon-based materials) to detect excretion-secretion antigens from the parasite Tritrichomonas foetus, which produces a disease called bovine trichomonosis. Automation tools will help make the experiments more reproducible, faster, and less dependent on manual work. I would use a liquid-handling robot (for example the Opentrons OT-2) to automate repetitive lab tasks, such as preparing nanoparticle solutions, mixing reagents, functionalizing nanoparticles with antibodies or aptamers, performing washing steps, preparing assay plates, etc. this would allow testing many conditions at the same time (for example, different nanoparticle types or concentrations) to find the best sensor design. Automation could also be used to test the biosensor performance, maybe by adding samples and controls to plates, preparing serial dilutions of the target antigen, running multiple detection assays in parallel, measuring signals, etc. that would help evaluate sensitivity and specificity of the sensor more efficiently. I also plan to design simple 3D-printed holders to organize tubes, microplates or sensor chips on the robot deck. If available, the Ginkgo Nebula platform could be used to screen different antibodies or binding molecules to find the one that recognizes the parasite protein with the highest specificity, improving the performance of the biosensor.