ENRICH-iST Workflow on the Biomek i7 Hybrid Workstation
High-resolution plasma proteomics by LC-MS is inherently challenged by the extreme dynamic range of protein abundances and the need for robust, scalable sample preparation. To address these limitations, we implemented and validated a fully automated ENRICH-iST workflow on the Biomek i7 Hybrid Workstation, enabling standardized, high-throughput plasma processing for large cohort studies.
End-to-End Automation of Plasma Sample Preparation
The workflow integrates magnetic bead-based enrichment with on-deck thermal control and positive pressure-driven solid phase extraction (SPE), enabling a seamless and reproducible process from plasma input to MS-ready peptides.
Key automated process steps include:
- Bead preparation and washing using magnetic separation
- Protein enrichment via controlled binding conditions
- On-deck lysis and enzymatic digestion
- Positive pressure SPE-based peptide purification
- Optional automated fluorometric peptide quantification
The system is configured with integrated modules, including a shaker, incubator, magnetic plate, and a positive pressure unit, allowing full process execution without manual intervention up to the clean peptide stage.
High-Throughput Capability and Workflow Efficiency
The automated setup enables the parallel processing of up to 96 plasma samples within approximately 6 hours, significantly reducing hands-on time while maintaining strict process consistency.
Custom-designed labware carriers developed at the Center for Life Science Automation (celisca) ensure reliable handling of ENRICH-iST kit components and seamless integration into the liquid handling workflow. The combination of Span-8 and multichannel pipetting further accelerates liquid transfer steps and enhances throughput.
Analytical Performance and Reproducibility
The performance of the automated workflow was benchmarked against manual sample preparation using LC-MS analysis (timsTOF HT, dia-PASEF acquisition).
Key observations include:
- Increased protein identifications compared to manual workflows
- Comparable intra-plate variability, demonstrating robust process control
- Negligible signal in blank samples, indicating absence of cross-contamination
- Consistent peptide recovery and quantification across the plate
The enrichment strategy effectively reduces the dynamic range of plasma proteins, enabling deeper proteome coverage and improved detection of low-abundance biomarkers.
Scalable Solution for Proteomics Applications
The automated ENRICH-iST workflow provides a standardized and scalable solution for:
- Large-scale biomarker discovery studies
- Clinical proteomics and translational research
- High-throughput screening of plasma cohorts
By minimizing manual intervention and variability, the system ensures reproducibility across batches and operators—critical for data-driven proteomics and regulated environments.
Conclusion
The integration of ENRICH-iST sample preparation with the Biomek i7 platform establishes a robust, high-throughput workflow for plasma proteomics. The combination of automation, enrichment efficiency, and reproducible performance significantly enhances analytical depth while enabling scalable processing of large sample cohorts.
