Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.
Ulises H GuzmanAna Martínez-ValZilu YeEugen DamocTabiwang N ArreyAnna PashkovaSantosh RenuseEduard DenisovJohannes PetzoldtAmelia C PetersonFlorian HarkingOle ØstergaardRasmus RydbirkSusana AznarHamish StewartYue XuanDaniel HermansonStevan HorningChristian HockAlexander A MakarovVlad ZabrouskovJesper Velgaard OlsenPublished in: Nature biotechnology (2024)
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th 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 which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.
Keyphrases
- mass spectrometry
- high resolution
- ms ms
- liquid chromatography
- endothelial cells
- high performance liquid chromatography
- gas chromatography
- capillary electrophoresis
- label free
- tandem mass spectrometry
- induced pluripotent stem cells
- multiple sclerosis
- electronic health record
- high resolution mass spectrometry
- computed tomography
- pluripotent stem cells
- blood pressure
- magnetic resonance imaging
- ultra high performance liquid chromatography
- liquid chromatography tandem mass spectrometry
- small cell lung cancer
- simultaneous determination
- healthcare
- affordable care act
- data analysis
- electron microscopy
- contrast enhanced