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High-Throughput Proteomics Sample Preparation Using a 96-Channel Pipettor and Magnetic Pin Device.

Georgia Roumelioti1,2, Alex Montoya1,2, Gemma L M Fisher1,2

  • 1MRC Laboratory of Medical Sciences (LMS), London W12 0HS, U.K.

Journal of Proteome Research
|February 16, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces a streamlined 96-well workflow for robust phosphoproteomics, using manual pipetting devices to reduce complexity and cost. The method enables efficient sample processing, making high-throughput proteomics more accessible and paving the way for full automation.

Keywords:
PACSP3high-throughput sample preparationoasis HLBphosphoproteomicsproteomics

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • High-throughput proteomics, especially post-translational modification (PTM) profiling, faces challenges in automation, reproducibility, and cost.
  • Current automated workflows are often complex and expensive, limiting accessibility for many research labs.

Purpose of the Study:

  • To present a practical, cost-effective intermediate solution for reproducible phosphoproteomics using manually operated 96-channel devices.
  • To simplify and enhance the efficiency of sample processing in high-throughput proteomics.
  • To serve as a stepping stone towards full automation of proteomics workflows.

Main Methods:

  • Utilized a Gilson Platemaster P220 pipettor and VP Scientific 96-well magnetic pin device for manual operation.
  • Developed a cost-efficient method for generating 96-well solid-phase extraction plates using Oasis HLB sorbent.
  • Optimized protein aggregation capture (PAC/SP3) digestion by demonstrating that continuous bead suspension is not required.

Main Results:

  • Achieved robust and reproducible phosphoproteomics in a 96-well format within 2 days.
  • Successfully completed protein aggregation capture (PAC/SP3) digestion, desalting, phosphopeptide enrichment, and a second desalting step.
  • Characterized the performance of custom-packed 96-well solid-phase extraction plates for loading capacity, lipid removal, and fractionation suitability.
  • Demonstrated simplified PAC digestion by brief aspiration, eliminating the need for orbital shaking.

Conclusions:

  • The presented manual 96-channel workflow offers a practical and reproducible approach to phosphoproteomics.
  • Innovations in solid-phase extraction plate generation and digestion methods reduce cost and complexity.
  • This workflow familiarizes users with 96-channel devices, facilitating a transition towards fully automated high-throughput proteomics.