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Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.
Guzman, Ulises H; Martinez-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.
Afiliação
  • Guzman UH; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
  • Martinez-Val A; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
  • Ye Z; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
  • Damoc E; 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.
  • Arrey TN; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Pashkova A; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Renuse S; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Denisov E; Thermo Fisher Scientific, San Jose, CA, USA.
  • Petzoldt J; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Peterson AC; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Harking F; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Østergaard O; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
  • Rydbirk R; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
  • Aznar S; Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
  • Stewart H; Centre for Neuroscience and Stereology, Copenhagen University Hospital, Copenhagen, Denmark.
  • Xuan Y; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Hermanson D; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Horning S; Thermo Fisher Scientific, San Jose, CA, USA.
  • Hock C; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Makarov A; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Zabrouskov V; Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
  • Olsen JV; Thermo Fisher Scientific, San Jose, CA, USA.
Nat Biotechnol ; 2024 Feb 01.
Article em En | MEDLINE | ID: mdl-38302753
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.

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Nat Biotechnol Assunto da revista: BIOTECNOLOGIA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Dinamarca

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Nat Biotechnol Assunto da revista: BIOTECNOLOGIA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Dinamarca