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Related Experiment Video

Updated: Oct 13, 2025

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot
10:12

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

Published on: October 28, 2021

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

Yu Han1, Cody T Thomas1, Sara A Wennersten1

  • 1Department of Medicine-Cardiology, University of Colorado Anschutz Medical Campus; Consortium for Fibrosis Research & Translation, School of Medicine, University of Colorado Anschutz Medical Campus.

Journal of Visualized Experiments : Jove
|November 15, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces an affordable, open-source automation system for mass spectrometry proteomics sample preparation. The Opentrons OT-2 robot streamlines protein digestion and clean-up, enhancing reproducibility and reducing manual labor in research labs.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Laboratory Automation

Background:

  • Mass spectrometry-based shotgun proteomics involves labor-intensive sample preparation steps.
  • Manual workflows are prone to batch-to-batch variability, impacting research reproducibility.
  • High costs of commercial automation systems limit accessibility for academic laboratories.

Purpose of the Study:

  • To present an affordable, open-source automation workflow for proteomics sample preparation.
  • To detail the setup of semi-automated protein reduction, alkylation, digestion, and clean-up using the Opentrons OT-2.
  • To provide open-source Python scripts for programming the automation system.

Main Methods:

  • Utilized the Opentrons OT-2, an open-source liquid handling robot.
  • Developed and implemented semi-automated protocols for key proteomics sample preparation steps.
  • Created custom Python scripts to control the OT-2 system via its API.

Main Results:

  • Successfully adapted the Opentrons OT-2 for multi-step proteomics sample preparation.
  • Demonstrated the potential for reduced hands-on time and increased throughput.
  • Established a reproducible workflow amenable to academic research settings.

Conclusions:

  • The Opentrons OT-2 offers a cost-effective solution for automating proteomics sample preparation.
  • Open-source automation can enhance accessibility and reproducibility in proteomics research.
  • This workflow empowers academic labs to adopt automated sample preparation.