Ultrahigh-Throughput LC-MS/MS Method for Targeted Protein Degradation Compound Screening

A method developed in 2026 enables screening 300 samples per day using the Orbitrap Astral mass spectrometer. The dataset, created by Hanfeng Lin and shared on figshare, contains results identifying nearly 8000 protein groups from a single cell line with high reproducibility. It includes quantitation accuracy validation from multi-species mixture experiments and dose-response studies of degraders like pomalidomide.

Use Cases

• Validate method reproducibility for high-throughput proteomics based on the reported coefficient of variation of less than 10%.
• Assess quantitation accuracy for protein abundance changes based on the described multi-species mixture experiments with high R² values.
• Screen drug libraries for novel degraders based on the described 300 samples per day ultrahigh-throughput workflow.
• Study dose-dependent protein degradation patterns based on the analysis of compounds like pomalidomide, iberdomide, and mezigdomide.

Strengths

• Method achieves a throughput of 300 samples per day.
• Identifies close to 8000 protein groups from a single cell line.
• Reports a coefficient of variation (CV) of less than 10%, indicating high reproducibility.
• Quantitation accuracy demonstrated with an R² of 0.999 in a two-proteome mixture experiment.

Limitations

• Dataset size is only 11.8 KB, indicating a very limited scope, likely containing summary results or method parameters rather than raw screening data.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale analysis.

Provenance

Source

figshare

Collection Method

Developed LC-MS/MS method using an Orbitrap Astral mass spectrometer for screening targeted protein degradation compounds.

Freshness

Last updated 2026-05-06 05:04:42; freshness should be verified.