Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Noah M. Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M. Peters-Clarke, Caroline Fecher, Andrew J. Smith, Evgenia Shishkova, Tabiwang N. Arrey, Anna Pashkova, Margaret Lea Robinson, Nicholas Arp, Jing Fan, Juli Hansen, Andrea Galmozzi, Lia R. Serrano, Julie Rojas, Audrey P. Gasch, Michael S. Westphall, Hamish Stewart, Christian Hock, Eugen Damoc, David J. Pagliarini, Vlad Zabrouskov and Joshua J. Coon ()
Additional contact information
Noah M. Lancaster: University of Wisconsin-Madison
Pavel Sinitcyn: Morgridge Institute for Research
Patrick Forny: Washington University School of Medicine
Trenton M. Peters-Clarke: University of Wisconsin-Madison
Caroline Fecher: Washington University School of Medicine
Andrew J. Smith: Washington University School of Medicine
Evgenia Shishkova: University of Wisconsin-Madison
Tabiwang N. Arrey: Thermo Fisher Scientific (Bremen) GmbH
Anna Pashkova: Thermo Fisher Scientific (Bremen) GmbH
Margaret Lea Robinson: University of Wisconsin-Madison
Nicholas Arp: Morgridge Institute for Research
Jing Fan: Morgridge Institute for Research
Juli Hansen: University of Wisconsin-Madison, School of Medicine and Public Health
Andrea Galmozzi: University of Wisconsin-Madison
Lia R. Serrano: University of Wisconsin-Madison
Julie Rojas: University of Wisconsin-Madison
Audrey P. Gasch: University of Wisconsin-Madison
Michael S. Westphall: University of Wisconsin-Madison
Hamish Stewart: Thermo Fisher Scientific (Bremen) GmbH
Christian Hock: Thermo Fisher Scientific (Bremen) GmbH
Eugen Damoc: Thermo Fisher Scientific (Bremen) GmbH
David J. Pagliarini: Washington University School of Medicine
Vlad Zabrouskov: Thermo Fisher Scientific
Joshua J. Coon: University of Wisconsin-Madison

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

Date: 2024
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DOI: 10.1038/s41467-024-51274-0

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