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Deep and fast label-free Dynamic Organellar Mapping

Author

Listed:
  • Julia P. Schessner

    (Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry)

  • Vincent Albrecht

    (Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry)

  • Alexandra K. Davies

    (Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry
    University of Manchester)

  • Pavel Sinitcyn

    (Max-Planck Institute of Biochemistry)

  • Georg H. H. Borner

    (Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry)

Abstract

The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we enhance the performance of DOMs through data-independent acquisition (DIA) mass spectrometry. DIA-DOMs achieve twice the depth of our previous workflow in the same mass spectrometry runtime, and substantially improve profiling precision and reproducibility. We leverage this gain to establish flexible map formats scaling from high-throughput analyses to extra-deep coverage. Furthermore, we introduce DOM-ABC, a powerful and user-friendly open-source software tool for analyzing profiling data. We apply DIA-DOMs to capture subcellular localization changes in response to starvation and disruption of lysosomal pH in HeLa cells, which identifies a subset of Golgi proteins that cycle through endosomes. An imaging time-course reveals different cycling patterns and confirms the quantitative predictive power of our translocation analysis. DIA-DOMs offer a superior workflow for label-free spatial proteomics as a systematic phenotype discovery tool.

Suggested Citation

  • Julia P. Schessner & Vincent Albrecht & Alexandra K. Davies & Pavel Sinitcyn & Georg H. H. Borner, 2023. "Deep and fast label-free Dynamic Organellar Mapping," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41000-7
    DOI: 10.1038/s41467-023-41000-7
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    References listed on IDEAS

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    1. Ana Martinez-Val & Dorte B. Bekker-Jensen & Sophia Steigerwald & Claire Koenig & Ole Østergaard & Adi Mehta & Trung Tran & Krzysztof Sikorski & Estefanía Torres-Vega & Ewa Kwasniewicz & Sólveig Hlín B, 2021. "Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    2. Alexandra K. Davies & Julian E. Alecu & Marvin Ziegler & Catherine G. Vasilopoulou & Fabrizio Merciai & Hellen Jumo & Wardiya Afshar-Saber & Mustafa Sahin & Darius Ebrahimi-Fakhari & Georg H. H. Borne, 2022. "AP-4-mediated axonal transport controls endocannabinoid production in neurons," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Alexandra K. Davies & Daniel N. Itzhak & James R. Edgar & Tara L. Archuleta & Jennifer Hirst & Lauren P. Jackson & Margaret S. Robinson & Georg H. H. Borner, 2018. "AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A," Nature Communications, Nature, vol. 9(1), pages 1-21, December.
    4. Won-Ki Huh & James V. Falvo & Luke C. Gerke & Adam S. Carroll & Russell W. Howson & Jonathan S. Weissman & Erin K. O'Shea, 2003. "Global analysis of protein localization in budding yeast," Nature, Nature, vol. 425(6959), pages 686-691, October.
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    Cited by:

    1. Kopalle, Praveen K. & Pauwels, Koen & Akella, Laxminarayana Yashaswy & Gangwar, Manish, 2023. "Dynamic pricing: Definition, implications for managers, and future research directions," Journal of Retailing, Elsevier, vol. 99(4), pages 580-593.
    2. Ying Zhu & Kerem Can Akkaya & Julia Ruta & Nanako Yokoyama & Cong Wang & Max Ruwolt & Diogo Borges Lima & Martin Lehmann & Fan Liu, 2024. "Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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