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

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

  • Zilu Ye
  • Eugen Damoc
  • Tabiwang N. Arrey
  • Anna Pashkova
  • Santosh Renuse
  • Eduard Denisov
  • Johannes Petzoldt
  • Amelia C. Peterson
  • Florian Harking
  • Susana Aznar
  • Hamish Stewart
  • Yue Xuan
  • Daniel Hermanson
  • Stevan Horning
  • Christian Hock
  • Alexander Makarov
  • Vlad Zabrouskov

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.

OriginalsprogEngelsk
TidsskriftNature Biotechnology
ISSN1087-0156
DOI
StatusE-pub ahead of print - 2024

Bibliografisk note

Funding Information:
We thank the MRC London Brain Bank for Neurodegenerative Diseases for providing some of the samples for the present study. J.V.O. acknowledges funding from the Novo Nordisk Foundation under grant no. NNF14CC0001. The Novo Nordisk Foundation’s Copenhagen Bioscience PhD Program (grant no. NNF16CC0020906) supported U.H.G. The proteomics technology developments applied were part of a project that has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement nos. MSmed-686547, EPIC-XS-823839 and PUSHH-861389, and ERC synergy grant no. HighResCells-810057. Z.Y. was supported by the Non-profit Central Research Institute Fund of the Chinese Academy of Medical Sciences (grant no. 2023-RC180-03), the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (2022-I2M-2-004) and the NCTIB Fund for the R&D Platform for Cell and Gene Therapy.

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

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