Ultra-fast label-free quantification andcomprehensive proteome coveragewith narrow-window data-independentacquisition. DIA/DDA comparison

ABSTRACT: Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependent and independent methods. This is achieved by pairing a Quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer that provides >200 Hz MS/MS scanning speed, high resolving power and sensitivity, as well as low ppm-mass accuracy. Narrowwindow DIA enables profiling of up to 100 full yeast proteomes per day, or ~10,000 human proteins in half-an-hour. Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. High quantitative precision and accuracy is demonstrated with high peptide coverage in a 3-species proteome mixture, quantifying 14,000+ proteins in a single run in half-an-hour.

INSTRUMENT(S): Thermo Finnigan instrument model

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ulises H Guzman  

LAB HEAD: Jesper V

PROVIDER: PXD046377 | Pride | 2024-02-01

REPOSITORIES: Pride