Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth

Guzman, U. H.; Martinez del Val, A.; Ye, Z.; Damoc, E.; Arrey, T. N.; Pashkova, A.; Denisov, E.; Petzoldt, J.; Peterson, A. C.; Harking, F.; Ostergaard, O.; Stewart, H.; Xuan, Y.; Hermanson, D.; Hock, C.; Makarov, A. A.; Zabrouskov, V.; Olsen, J. V.

doi:10.1101/2023.06.02.543374

bioRxiv · 10.1101/2023.06.02.543374

Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth

Guzman, U. H.·Martinez del Val, A.·Ye, Z.·Damoc, E.·Arrey, T. N.·Pashkova, A.·Denisov, E.·Petzoldt, J.·Peterson, A. C.·Harking, F.·Ostergaard, O.·Stewart, H.·Xuan, Y.·Hermanson, D.·Hock, C.·Makarov, A. A.·Zabrouskov, V.·Olsen, J. V.

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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. Narrow-window 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. TeaserAccurate and precise label-free quantification with comprehensive proteome coverage using narrow-window DIA

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Guzman, U. H., Martinez del Val, A., Ye, Z., Damoc, E., Arrey, T. N., Pashkova, A., Denisov, E., Petzoldt, J., Peterson, A. C., Harking, F., Ostergaard, O., Stewart, H., Xuan, Y., Hermanson, D., Hock, C., Makarov, A. A., Zabrouskov, V., Olsen, J. V.. 2023-06-06. Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. https://doi.org/10.1101/2023.06.02.543374

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