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Introduction
Modern drug discovery efforts are complex. Clinical research is a high-stakes, fast-paced process—from uncovering novel targets to bringing effective therapies to market. To accelerate this journey, scientists are turning to cutting-edge technologies such as proteomics, which provides powerful insights into disease mechanisms, drug responses, and biomarker identification at the protein level.
Proteomics bridges the gap between genomics and functional biology, offering a mechanism-driven view of drug-target interactions. But as the scale of discovery grows—driven by high-throughput screening (HTS) and multi-omics integration—the bottleneck of sample preparation becomes increasingly apparent.
While compound screening has benefited immensely from automation, proteomic sample preparation remains a time-consuming, variable, and labor-intensive process. Without standardization and scalability, valuable data quality and reproducibility are put at risk.
Challenges: Sample Preparation in the Era of High-Throughput Drug Discovery
Drug discovery workflows are becoming faster and more data-driven. But with millions of samples and small molecules to test, traditional sample preparation methods are increasingly unfit for purpose. Key challenges include:
● Volume and scale: Processing thousands of biological samples quickly and reproducibly is critical.
● Data integrity: Manual workflows introduce variability that undermines downstream mass spectrometry (MS) analysis.
● Time pressure: Rapid development timelines demand efficient, reliable workflows.
● Labor burden: Repetitive pipetting and handling slow productivity and increase human error. Conventional sample preparation workflows—cell lysis, reduction, alkylation, digestion, and cleanup—are not only time-consuming but also difficult to scale, making it a major hurdle for high-throughput proteomics.
Solution: Automating Sample Preparation with PreOmics® Technologies
To meet the needs of high-throughput drug discovery, PreOmics® offers a wide range of fully automatable, scalable, and standardized proteomics solutions that deliver both speed and precision—without compromise.
iST Technology: Fast, Flexible, Reproducible
The in-StageTip (iST) workflow streamlines proteomics sample preparation into a simple three-step process—from raw biological samples to clean peptides ready for LC-MS. Key advantages include:
● Preparation time reduced from ~48 hours to just 2 hours
● Supports diverse input types and concentrations (1–100 µg protein)
● Processes up to 96 samples per batch
● Reproducible and automation-compatible
iST ensures consistent sample processing across cell types, tissues, and biofluids—perfect for hit validation and mechanism-of-action studies.
ENRICH Technology: Powering Plasma, Serum, and CSF Proteomics
Proteomic analysis of biofluids like plasma or cerebrospinal fluid (CSF) is notoriously challenging due to the wide dynamic range of protein concentrations and low abundance of potential biomarkers. PreOmics® ENRICH technology compresses the dynamic range using paramagnetic bead-based enrichment, allowing for:
● Deeper proteome coverage
● 8x increase in protein identifications
● Reproducibility across large cohorts (CV <14%)
● Seamlessly integrated into established lab automation platforms
ENRICH prepares raw samples to MS-ready peptides in under five hours—ideal for biomarker discovery and longitudinal studies.
Case Studies: High-Throughput Success in Action
Large-Cohort Proteomics for Drug Efficacy Evaluation
In a recent study, the iST workflow was fully automated on the APP96™ platform, enabling high-throughput analysis of diverse sample types:
● Mammalian cells (HeLa, HEK), insect cells (H5), yeast, and human blood plasma
● Thousands of proteins quantified per sample
● Exceptional run-to-run reproducibility
This end-to-end automated solution supports drug efficacy screening at scale—delivering deep, reliable insights for mechanism-of-action studies and therapeutic candidate selection.
Deep Plasma Profiling with ENRICH
Plasma proteomics using ENRICH revealed an 8-fold increase in protein identifications over neat plasma. In a 30-replicate study:
● Median coefficient of variation(CV) <14%
● 4.5x greater overlap with the Human Proteome Atlas for blood
This level of coverage enabled detection of trace-level biomarkers—often missed by conventional methods—making ENRICH a transformative tool for biomarker discovery and early-stage drug validation.
Conclusion
Drug discovery processes require speed, precision, and reproducibility to drive competitive advantages. Automated proteomics sample preparation is increasingly necessary for a wide range of short and long term clinical trials. PreOmics® technologies like iST and ENRICH empower scientists to move faster, scale higher, and deliver more reliable results across every stage of the drug development pipeline.
From uncovering molecular mechanisms to validating lead candidates, PreOmics® helps turn complex biological data into actionable therapeutic insights—at the pace modern drug discovery demands. If you would like to learn more about innovating drug discovery processes, refer to our webinar on transforming biomedicine through proteomics.
