Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Lancaster, Noah M.; Sinitcyn, Pavel; Forny, Patrick; Peters-Clarke, Trenton M.; Fecher, Caroline; Smith, Andrew J.; Shishkova, Evgenia; Arrey, Tabiwang N.; Pashkova, Anna; Robinson, Margaret Lea; Arp, Nicholas; Fan, Jing; Hansen, Juli; Galmozzi, Andrea; Serrano, Lia R.; Rojas, Julie; Gasch, Audrey P.; Westphall, Michael S.; Stewart, Hamish; Hock, Christian; Damoc, Eugen; Pagliarini, David J.; Zabrouskov, Vlad; Coon, Joshua J.

doi:10.1038/s41467-024-51274-0

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Journal Article · Thu Aug 15 04:00:00 EDT 2024 · Nature Communications

DOI:https://doi.org/10.1038/s41467-024-51274-0· OSTI ID:2473060

^[1]; ^[2]; ^[3]; ^[4]; ^[3]; ^[3]; ^[5]; Arrey, Tabiwang N. ^[6]; Pashkova, Anna ^[6]; Robinson, Margaret Lea ^[4]; ^[7]; ^[7]; Hansen, Juli ^[8]; ^[8]; Serrano, Lia R. ^[8]; Rojas, Julie ^[8]; ^[8]; Westphall, Michael S. ^[9]; Stewart, Hamish ^[6]; Hock, Christian ^[6] more »

University of Wisconsin-Madison, Madison, WI (United States); University of Wisconsin-Madison Department of Biomolecular Chemistry
Morgridge Institute for Research, Madison, WI (United States)
Washington University School of Medicine, St. Louis, MO (United States)
University of Wisconsin-Madison, Madison, WI (United States)
University of Wisconsin-Madison, Madison, WI (United States); National Center for Quantitative Biology of Complex Systems, Madison, WI (United States)
Thermo Fisher Scientific (Bremen) GmbH, Bremen (Germany)
Morgridge Institute for Research, Madison, WI (United States); University of Wisconsin-Madison, WI (United States)
University of Wisconsin-Madison, WI (United States)
University of Wisconsin-Madison, WI (United States); National Center for Quantitative Biology of Complex Systems, Madison, WI (United States)
Thermo Fisher Scientific, San Jose, CA (United States)
University of Wisconsin-Madison, WI (United States); Morgridge Institute for Research, Madison, WI (United States); National Center for Quantitative Biology of Complex Systems, Madison, WI (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018409

OSTI ID:: 2473060

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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A data-independent acquisition-based global phosphoproteomics system enables deep profiling

Journal Article · Wed May 05 00:00:00 EDT 2021 · Nature Communications · OSTI ID:1815690

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

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