The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.
Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition
Open accessAbstract
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.
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Cites
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DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
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Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
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Self-citationCORUM: the comprehensive resource of mammalian protein complexes—2009
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Higher-energy C-trap dissociation for peptide modification analysis
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Cited by
Skowronek, P., Wallmann, G., Wahle, M., Willems, S., & Mann, M. (2025) · Nature Protocols · doi:10.1038/s41596-024-01104-w · Cited by 43
Global analysis of protein turnover dynamics in single cells
Sabatier, P., Lechner, M., Guzmán, U. H., Beusch, C. M., Zeng, X., Wang, L., Izaguirre, F., Seth, A., Gritsenko, O., Rodin, S., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.002 · Cited by 41
Self-citationUnbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics
Steger, M., Nishiguchi, G., Wu, Q., Schwalb, B., Shashikadze, B., McGowan, K., Actis, M., Aggarwal, A., Shi, Z., Price, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62829-0 · Cited by 32
Single-cell proteomic landscape of the developing human brain
Wu, T., Jiang, L., Mukhtar, T., Wang, L., Jian, R., Wang, C., Trinh, T., Kriegstein, A. R., Snyder, M., & Li, J. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02980-7 · Cited by 23
(2025) · doi:10.1038/s41594-025-01699-y · Cited by 8
Metadata
- Authors
- Guzman, U. H., Martinez-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., Makarov, A., Zabrouskov, V., & Olsen, J. V.
- Venue
- Nature Biotechnology
- Published
- 2024-02-01
- Volume
- 42
- Issue
- 12
- Pages
- 1855-1866
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W4391437651
- Cited by
- 346
- References
- 59
- FWCI
- 41.49
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Guzman, U. H., Martinez-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
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