High-throughput proteomics sample preparation using a 96-channel pipettor and magnetic pin device
Author(s)
Type
Journal Article
Abstract
High-throughput proteomics requires efficient and highly reproducible sample processing, yet workflows─particularly for PTM profiling─remain complex and costly to fully automate. Here, we present a practical intermediate solution using manually operated 96-channel devices: the Gilson Platemaster P220 pipettor and VP Scientific 96-well magnetic pin device. Using this setup, we achieved robust and reproducible phosphoproteomics in a 96-well format, completing protein aggregation capture (PAC/SP3) digestion, desalting, phosphopeptide enrichment, and a second desalting step within 2 days while minimizing operator workload and variability. Several innovations enable this workflow. First, we describe a cost-efficient method to generate 96-well solid-phase extraction plates by directly packing the Oasis HLB sorbent into tapered filter plates. We extensively characterize these plates in terms of loading capacity, lipid removal efficiency, and suitability for high-pH fractionation. Second, we demonstrate that efficient PAC digestion does not require continuous bead suspension; instead, digestion can be achieved by briefly aspirating beads in protease solution, eliminating the need for orbital shaking and simplifying automation. The presented workflow familiarizes users with 96-channel devices and hence serves as a good step toward full automation.
Date Issued
2026-03-06
Date Acceptance
2026-01-12
Citation
Journal of Proteome Research, 2026, 25 (3), pp.1647-1661
ISSN
1535-3893
Publisher
American Chemical Society
Start Page
1647
End Page
1661
Journal / Book Title
Journal of Proteome Research
Volume
25
Issue
3
Copyright Statement
© 2026 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0 .
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41693659
Subjects
PAC
SP3
high-throughput sample preparation
oasis HLB
phosphoproteomics
proteomics
Proteomics
Phosphopeptides
Humans
High-Throughput Screening Assays
Workflow
Solid Phase Extraction
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2026-02-16