Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Hybrid-DIA : intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. / Martínez-Val, Ana; Fort, Kyle; Koenig, Claire; Van der Hoeven, Leander; Franciosa, Giulia; Moehring, Thomas; Ishihama, Yasushi; Chen, Yu ju; Makarov, Alexander; Xuan, Yue; Olsen, Jesper V.

In: Nature Communications, Vol. 14, 3599, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Martínez-Val, A, Fort, K, Koenig, C, Van der Hoeven, L, Franciosa, G, Moehring, T, Ishihama, Y, Chen, YJ, Makarov, A, Xuan, Y & Olsen, JV 2023, 'Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids', Nature Communications, vol. 14, 3599. https://doi.org/10.1038/s41467-023-39347-y

APA

Martínez-Val, A., Fort, K., Koenig, C., Van der Hoeven, L., Franciosa, G., Moehring, T., Ishihama, Y., Chen, Y. J., Makarov, A., Xuan, Y., & Olsen, J. V. (2023). Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nature Communications, 14, [3599]. https://doi.org/10.1038/s41467-023-39347-y

Vancouver

Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T et al. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nature Communications. 2023;14. 3599. https://doi.org/10.1038/s41467-023-39347-y

Author

Martínez-Val, Ana ; Fort, Kyle ; Koenig, Claire ; Van der Hoeven, Leander ; Franciosa, Giulia ; Moehring, Thomas ; Ishihama, Yasushi ; Chen, Yu ju ; Makarov, Alexander ; Xuan, Yue ; Olsen, Jesper V. / Hybrid-DIA : intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. In: Nature Communications. 2023 ; Vol. 14.

Bibtex

@article{6bcbf4db6e74475caf0c7326102b513b,
title = "Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids",
abstract = "Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.",
author = "Ana Mart{\'i}nez-Val and Kyle Fort and Claire Koenig and {Van der Hoeven}, Leander and Giulia Franciosa and Thomas Moehring and Yasushi Ishihama and Chen, {Yu ju} and Alexander Makarov and Yue Xuan and Olsen, {Jesper V.}",
note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
doi = "10.1038/s41467-023-39347-y",
language = "English",
volume = "14",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Hybrid-DIA

T2 - intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

AU - Martínez-Val, Ana

AU - Fort, Kyle

AU - Koenig, Claire

AU - Van der Hoeven, Leander

AU - Franciosa, Giulia

AU - Moehring, Thomas

AU - Ishihama, Yasushi

AU - Chen, Yu ju

AU - Makarov, Alexander

AU - Xuan, Yue

AU - Olsen, Jesper V.

N1 - Publisher Copyright: © 2023, The Author(s).

PY - 2023

Y1 - 2023

N2 - Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.

AB - Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.

U2 - 10.1038/s41467-023-39347-y

DO - 10.1038/s41467-023-39347-y

M3 - Journal article

C2 - 37328457

AN - SCOPUS:85162073632

VL - 14

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 3599

ER -

ID: 360682205