PMID- 38302753
OWN - NLM
STAT- Publisher
LR  - 20240201
IS  - 1546-1696 (Electronic)
IS  - 1087-0156 (Linking)
DP  - 2024 Feb 1
TI  - Ultra-fast label-free quantification and comprehensive proteome coverage with 
      narrow-window data-independent acquisition.
LID - 10.1038/s41587-023-02099-7 [doi]
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 3x 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.
CI  - (c) 2024. The Author(s).
FAU - Guzman, Ulises H
AU  - Guzman UH
AUID- ORCID: 0000-0003-1665-7659
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark.
FAU - Martinez-Val, Ana
AU  - Martinez-Val A
AUID- ORCID: 0000-0002-8784-3822
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark.
FAU - Ye, Zilu
AU  - Ye Z
AUID- ORCID: 0000-0001-8829-6579
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark.
AD  - State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou 
      Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union 
      Medical College, Suzhou, China.
FAU - Damoc, Eugen
AU  - Damoc E
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Arrey, Tabiwang N
AU  - Arrey TN
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Pashkova, Anna
AU  - Pashkova A
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Renuse, Santosh
AU  - Renuse S
AD  - Thermo Fisher Scientific, San Jose, CA, USA.
FAU - Denisov, Eduard
AU  - Denisov E
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Petzoldt, Johannes
AU  - Petzoldt J
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Peterson, Amelia C
AU  - Peterson AC
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Harking, Florian
AU  - Harking F
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark.
FAU - Ostergaard, Ole
AU  - Ostergaard O
AUID- ORCID: 0000-0003-3160-8548
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark.
FAU - Rydbirk, Rasmus
AU  - Rydbirk R
AUID- ORCID: 0000-0002-4670-7533
AD  - Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of 
      Biochemistry and Molecular Biology, University of Southern Denmark, Odense, 
      Denmark.
FAU - Aznar, Susana
AU  - Aznar S
AUID- ORCID: 0000-0001-7940-6246
AD  - Centre for Neuroscience and Stereology, Copenhagen University Hospital, 
      Copenhagen, Denmark.
FAU - Stewart, Hamish
AU  - Stewart H
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Xuan, Yue
AU  - Xuan Y
AUID- ORCID: 0000-0001-9132-2643
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Hermanson, Daniel
AU  - Hermanson D
AD  - Thermo Fisher Scientific, San Jose, CA, USA.
FAU - Horning, Stevan
AU  - Horning S
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Hock, Christian
AU  - Hock C
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Makarov, Alexander
AU  - Makarov A
AUID- ORCID: 0000-0002-7046-6709
AD  - Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
FAU - Zabrouskov, Vlad
AU  - Zabrouskov V
AD  - Thermo Fisher Scientific, San Jose, CA, USA.
FAU - Olsen, Jesper V
AU  - Olsen JV
AUID- ORCID: 0000-0002-4747-4938
AD  - Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 
      Copenhagen, Denmark. jesper.olsen@cpr.ku.dk.
LA  - eng
GR  - NNF14CC0001/Novo Nordisk Fonden (Novo Nordisk Foundation)/
GR  - NNF16CC0020906/Novo Nordisk Fonden (Novo Nordisk Foundation)/
GR  - MSmed-686547/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - EPIC-XS-823839/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - PUSHH-861389/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - HighResCells-810057/EC | EU Framework Programme for Research and Innovation H2020 
      | H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - PUSHH-861389/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - MSmed-686547/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - MSmed-686547/EC | EU Framework Programme for Research and Innovation H2020 | 
      H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
PT  - Journal Article
DEP - 20240201
PL  - United States
TA  - Nat Biotechnol
JT  - Nature biotechnology
JID - 9604648
SB  - IM
EDAT- 2024/02/02 00:42
MHDA- 2024/02/02 00:42
CRDT- 2024/02/01 23:53
PHST- 2023/06/14 00:00 [received]
PHST- 2023/12/13 00:00 [accepted]
PHST- 2024/02/02 00:42 [medline]
PHST- 2024/02/02 00:42 [pubmed]
PHST- 2024/02/01 23:53 [entrez]
AID - 10.1038/s41587-023-02099-7 [pii]
AID - 10.1038/s41587-023-02099-7 [doi]
PST - aheadofprint
SO  - Nat Biotechnol. 2024 Feb 1. doi: 10.1038/s41587-023-02099-7.