In a recent preprint, “Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics,” a team led by Dr. Salla Keskitalo and colleagues at the University of Helsinki presents an impressive achievement: a fully automated, cost-effective plasma proteomics workflow that runs from raw sample to LC-MS injection—powered by Evosep One.
Their study highlights not only the power of scalable enrichment techniques like MagNet but also the critical role automation plays in large-cohort proteomic studies. The team successfully integrated automated sample prep, digestion, and Evotip loading using a Biomek i5 liquid handler—enabling reproducible processing of full 96-well plates with minimal hands-on time.
“Combining the Evosep One and Evotip with the Biomek i5 for high-throughput plasma proteomics has given us a scalable and reliable workflow. The integration between Evosep One and our automated sample preparation is seamless—it’s truly impressive. We’re now able to manage large-scale studies effortlessly. Plus, the low cost per sample makes this setup ideal for our biobank projects.” Said Dr. Salla Keskitalo.
A Leap Forward in Automated Plasma Enrichment
The researchers benchmarked five plasma enrichment methods and found that MagNet—based on strong anion-exchange magnetic beads—offered deep proteome coverage and excellent compatibility with automation. When combined with Evosep One’s standardized gradients (30, 60, and 100 samples per day), the team achieved over 4,200 proteins per sample using just a 44-minute gradient on the timsTOF Pro 2.
Evotip Automation: From Bottleneck to Breeze
One of the most notable advancements was the automation of Evotip loading, using a dedicated Evosep kit compatible with the Biomek platform. This step, often a labor-intensive bottleneck in high-throughput workflows, was fully integrated into the protocol—streamlining the handoff to LC-MS and ensuring consistent sample loading.
Results That Inspire Confidence
- Coefficients of variation for protein quantification were consistently below 20%.
- Correlation across replicate samples exceeded R > 0.98.
- The workflow was robust across two 96-well plate batches, with no observed batch effects.
- Peptide digestion efficiency was uniform and comparable to manual preparation.
Importantly, the cost per enriched sample was kept to just a few dollars—demonstrating that deep plasma proteomics can be both powerful and practical.
Scalable Proteomics for Real-World Cohorts
Dr. Keskitalo and her team are now well-positioned to analyze thousands of clinical plasma samples. Their automated, reproducible, and cost-efficient pipeline, anchored by Evosep One, exemplifies what’s possible when thoughtful method development meets robust LC-MS technology.
Read full publication here: https://www.biorxiv.org/content/10.1101/2025.05.06.652407v1
