Precision-Engineered Nano-Electrospray Emitters Enhance Ionization Efficiency for Trap-Assisted Direct Infusion Mass Spectrometry: Application in Plasma Alzheimer’s Disease Proteomics

Shotgun direct infusion mass spectrometry (DI-MS) enables high-throughput proteomics. Yet, its performance critically depends on nanospray emitter quality. We present here precision-engineered nanospray emitters with an optimized 4-degree emitter tip angle, designed for sensitive, reproducible, user-friendly, and compatible across mass spectrometry platforms that demonstrated enhanced ionization efficiency and spray stability, showing a 2.1-fold improvement in protein identification rates compared to commercial designs using digested HeLa cell protein extract. Using plasma samples from Alzheimer’s disease (AD) patients and controls depleted of the 14 most-abundant proteins, we performed a comprehensive trap-assisted DI-MS protein identification and precise quantification using both Orbitrap Exploris 480 (OE480) and Orbitrap Astral mass spectrometers. We consistently identified and quantified 190 proteins in AD plasma samples in 5 min trap-assisted DI-MS runs, with superior reproducibility and sensitivity on the Orbitrap Astral. Our analysis revealed several unreported disease-associated protein signatures, while confirming known AD biomarkers, with C5, C4BPA, and FAM135B as the protein combination with the highest potential as AD plasma biomarkers for the detection of the disease. The enhanced performance of these standardized engineered nanospray emitters over traditional DI-MS workflow establishes a robust and scalable platform for high-throughput clinical proteomics.