Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. / Guzman, Ulises H.; Martinez Del Val, Ana; Ye, Zilu; Damoc, Eugen; Arrey, Tabiwang N.; Pashkova, Anna; Renuse, Santosh; Denisov, Eduard; Petzoldt, Johannes; Peterson, Amelia C.; Harking, Florian; Østergaard, Ole; Rydbirk, Rasmus; Aznar, Susana; Stewart, Hamish; Xuan, Yue; Hermanson, Daniel; Horning, Stevan; Hock, Christian; Makarov, Alexander; Zabrouskov, Vlad; Olsen, Jesper V.

In: Nature Biotechnology, 2024.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Guzman, UH, Martinez Del Val, A, Ye, Z, Damoc, E, Arrey, TN, Pashkova, A, Renuse, S, Denisov, E, Petzoldt, J, Peterson, AC, Harking, F, Østergaard, O, Rydbirk, R, Aznar, S, Stewart, H, Xuan, Y, Hermanson, D, Horning, S, Hock, C, Makarov, A, Zabrouskov, V & Olsen, JV 2024, 'Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition', Nature Biotechnology. https://doi.org/10.1038/s41587-023-02099-7

APA

Guzman, U. H., Martinez Del Val, A., Ye, Z., Damoc, E., Arrey, T. N., Pashkova, A., Renuse, S., Denisov, E., Petzoldt, J., Peterson, A. C., Harking, F., Østergaard, O., Rydbirk, R., Aznar, S., Stewart, H., Xuan, Y., Hermanson, D., Horning, S., Hock, C., ... Olsen, J. V. (2024). Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nature Biotechnology. https://doi.org/10.1038/s41587-023-02099-7

Vancouver

Guzman UH, Martinez Del Val A, Ye Z, Damoc E, Arrey TN, Pashkova A et al. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nature Biotechnology. 2024. https://doi.org/10.1038/s41587-023-02099-7

Author

Guzman, Ulises H. ; Martinez Del Val, Ana ; Ye, Zilu ; Damoc, Eugen ; Arrey, Tabiwang N. ; Pashkova, Anna ; Renuse, Santosh ; Denisov, Eduard ; Petzoldt, Johannes ; Peterson, Amelia C. ; Harking, Florian ; Østergaard, Ole ; Rydbirk, Rasmus ; Aznar, Susana ; Stewart, Hamish ; Xuan, Yue ; Hermanson, Daniel ; Horning, Stevan ; Hock, Christian ; Makarov, Alexander ; Zabrouskov, Vlad ; Olsen, Jesper V. / Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. In: Nature Biotechnology. 2024.

Bibtex

@article{aa72db5552844ba5846ea7aeb6789905,
title = "Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition",
abstract = "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.",
author = "Guzman, {Ulises H.} and {Martinez Del Val}, Ana and Zilu Ye and Eugen Damoc and Arrey, {Tabiwang N.} and Anna Pashkova and Santosh Renuse and Eduard Denisov and Johannes Petzoldt and Peterson, {Amelia C.} and Florian Harking and Ole {\O}stergaard and Rasmus Rydbirk and Susana Aznar and Hamish Stewart and Yue Xuan and Daniel Hermanson and Stevan Horning and Christian Hock and Alexander Makarov and Vlad Zabrouskov and Olsen, {Jesper V.}",
note = "Publisher Copyright: {\textcopyright} 2024, The Author(s).",
year = "2024",
doi = "10.1038/s41587-023-02099-7",
language = "English",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

AU - Guzman, Ulises H.

AU - Martinez Del Val, Ana

AU - Ye, Zilu

AU - Damoc, Eugen

AU - Arrey, Tabiwang N.

AU - Pashkova, Anna

AU - Renuse, Santosh

AU - Denisov, Eduard

AU - Petzoldt, Johannes

AU - Peterson, Amelia C.

AU - Harking, Florian

AU - Østergaard, Ole

AU - Rydbirk, Rasmus

AU - Aznar, Susana

AU - Stewart, Hamish

AU - Xuan, Yue

AU - Hermanson, Daniel

AU - Horning, Stevan

AU - Hock, Christian

AU - Makarov, Alexander

AU - Zabrouskov, Vlad

AU - Olsen, Jesper V.

N1 - Publisher Copyright: © 2024, The Author(s).

PY - 2024

Y1 - 2024

N2 - 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.

AB - 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.

U2 - 10.1038/s41587-023-02099-7

DO - 10.1038/s41587-023-02099-7

M3 - Journal article

C2 - 38302753

AN - SCOPUS:85183725759

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

ER -

ID: 382500111