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Poster Presentations
Day 3, June 24（Tue.）
Room P (Maesato East, Foyer, Ocean Wing)
- 3P-PM-47
Gas-Phase-Fractionation Spectral Library-Enhanced DIA Mass Spectrometry for Rapid and Deep Plasma Proteomics
(1CLSMB, NTU, 2IoC, AS, 3MST-TiGP, AS, 4Thermo Fisher San Jose, 5Surgery, NTUH, 6Thermo Fisher Bremen, 7Internal Med., CSMUH, 8Surgery, NTUH and NTU, 9Internal Med., NTUH)
Sung-Liang Yu1, Yi-Ju Chen2, oKun-Hao Chang2,3, Jared Deyarmin4, Yi-Shuang Chuang2, Yi-Jing Hsiao2, Chong-Jen Yu5, Tabiwang Arrey6, Jana Richter6, Stephanie Samra4, Daniel Hermanson4, Gee-Chen Chang7, Jin-Shing Chen8, Pan-Chyr Yang9, Yu-Ju Chen2
We present a high-throughput proteomics pipeline utilizing a modified Thermo Scientific Orbitrap Astral mass spectrometer to overcome limited throughput and profiling depth in plasma biomarker discovery. The method balances sensitivity and throughput, achieving 60 samples per day with 23-minute gradients. Initial testing on 59 participants with early-stage lung cancer and healthy controls demonstrated remarkable results. Using Top14 immunodepletion and nanoparticle-based enrichment protocols, the pipeline identified over 2,500 proteins in depleted samples and nearly 5,000 in nanoparticle-enriched samples through combined library-free and gas-phase fractionation spectral library searches. Compared to conventional Orbitrap Lumos, the method achieved a 6.47-fold higher data generation speed (112.7 versus 17.4 protein groups per minute) while maintaining high quantification rates (63.3% of proteins quantified in over 90% of samples). A strong cross-instrument correlation (0.91) confirmed robust reproducibility and transferability. This high-throughput analysis significantly enhances profiling efficiency while increasing proteome depth, offering a powerful platform for early biomarker discovery applicable to large-scale studies such as the TALENT screening trial for 12,000 never-smokers.