Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, which can take up significant person-hours of bench labor and present a source of batch-to-batch variability. Lab automation with pipetting robots can...

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Bibliographic Details
Published in:	Journal of visualized experiments no. 176
Main Authors:	Han, Yu, Thomas, Cody T, Wennersten, Sara A, Lau, Edward, Lam, Maggie P Y
Format:	Journal Article
Language:	English
Published:	United States 28-10-2021
Subjects:	Automation Humans Laboratories Proteomics Reproducibility of Results Robotics Specimen Handling
Online Access:	Get more information
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Summary:	Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, which can take up significant person-hours of bench labor and present a source of batch-to-batch variability. Lab automation with pipetting robots can reduce manual work, maximize throughput, and increase research reproducibility. Still, the steep starting prices of standard automation stations make them unaffordable for many academic laboratories. This article describes a proteomics sample preparation workflow using an affordable, open-source automation system (The Opentrons OT-2), including instructions for setting up semi-automated protein reduction, alkylation, digestion, and clean-up steps; as well as accompanying open-source Python scripts to program the OT-2 system through its application programming interface.
ISSN:	1940-087X
DOI:	10.3791/63092