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Related Experiment Video

Updated: Nov 6, 2025

Microsampling in Targeted Mass Spectrometry-Based Protein Analysis of Low-Abundance Proteins
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Microsampling in Targeted Mass Spectrometry-Based Protein Analysis of Low-Abundance Proteins

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A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation.

Xinyue Liu1, Steven P Gygi1, Joao A Paulo1

  • 1Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.

Journal of the American Society for Mass Spectrometry
|May 5, 2021
PubMed
Summary
This summary is machine-generated.

We developed a semiautomated paramagnetic bead-based platform for isobaric tag sample preparation. This robot-assisted method provides reproducible protein profiling, enhancing high-throughput proteomics workflows.

Keywords:
FAIMSOpentronsRTSSP3TMTproautomation

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Area of Science:

  • Proteomics
  • Biotechnology
  • Automation

Background:

  • High-throughput mass spectrometry requires efficient sample processing.
  • Automation in upstream sample preparation often lags behind new analytical techniques.

Purpose of the Study:

  • To develop and implement a semiautomated paramagnetic bead-based platform for isobaric tag sample preparation.
  • To benchmark the robot-assisted platform against manual processing for protein abundance profiling.

Main Methods:

  • Semiautomated paramagnetic bead-based platform for TMTpro16-plex sample preparation.
  • Comparison of robot-assisted vs. manual processing of six yeast strains in triplicate.
  • Development of an interactive website for proteome profile exploration.
  • Provision of open-source automation templates for the opentrons OT-2 liquid handler.

Main Results:

  • Robot-assisted and manual processing yielded similar numbers of quantified proteins and peptides.
  • High reproducibility was observed in both processing methods.
  • An interactive website was created to visualize yeast proteome data.

Conclusions:

  • The semiautomated platform offers a versatile and affordable solution for reproducible protein profiling.
  • Open-source templates facilitate the automation of routine proteomics workflows.
  • This approach supports advances in mass spectrometry-based applications.