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Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies

Author

Listed:
  • Yue Xuan

    (Thermo Fisher Scientific GmbH)

  • Nicholas W. Bateman

    (Uniformed Services University and Walter Reed National Military Medical Center)

  • Sebastien Gallien

    (Thermo Fisher Scientific
    Precision Medicine Science Center)

  • Sandra Goetze

    (Institute of Translational Medicine, Department of Health Sciences and Technology
    Swiss Institute of Bioinformatics)

  • Yue Zhou

    (Thermo Fisher Scientific Co. Ltd)

  • Pedro Navarro

    (Thermo Fisher Scientific GmbH)

  • Mo Hu

    (Thermo Fisher Scientific Co. Ltd)

  • Niyati Parikh

    (Uniformed Services University and Walter Reed National Military Medical Center)

  • Brian L. Hood

    (Uniformed Services University and Walter Reed National Military Medical Center)

  • Kelly A. Conrads

    (Uniformed Services University and Walter Reed National Military Medical Center)

  • Christina Loosse

    (Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V.)

  • Reta Birhanu Kitata

    (Institute of Chemistry, Academia Sinica)

  • Sander R. Piersma

    (Cancer Center Amsterdam)

  • Davide Chiasserini

    (Cancer Center Amsterdam
    University of Manchester)

  • Hongwen Zhu

    (Chinese Academy of Sciences)

  • Guixue Hou

    (BGI-SHENZHEN, Beishan Road, Yantian District)

  • Muhammad Tahir

    (University of Southern Denmark)

  • Andrew Macklin

    (Princess Margaret Cancer Centre)

  • Amanda Khoo

    (Princess Margaret Cancer Centre)

  • Xiuxuan Sun

    (National Translational Science Center for Molecular Medicine
    Air Force Medical University)

  • Ben Crossett

    (The University of Sydney)

  • Albert Sickmann

    (Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V.
    Ruhr-Universität Bochum
    University of Aberdeen)

  • Yu-Ju Chen

    (Institute of Chemistry, Academia Sinica)

  • Connie R. Jimenez

    (Cancer Center Amsterdam)

  • Hu Zhou

    (Chinese Academy of Sciences)

  • Siqi Liu

    (BGI-SHENZHEN, Beishan Road, Yantian District)

  • Martin R. Larsen

    (University of Southern Denmark)

  • Thomas Kislinger

    (Princess Margaret Cancer Centre)

  • Zhinan Chen

    (National Translational Science Center for Molecular Medicine
    Air Force Medical University)

  • Benjamin L. Parker

    (The University of Sydney)

  • Stuart J. Cordwell

    (The University of Sydney)

  • Bernd Wollscheid

    (Institute of Translational Medicine, Department of Health Sciences and Technology
    Swiss Institute of Bioinformatics)

  • Thomas P. Conrads

    (Women’s Service Line, Inova Health System)

Abstract

Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrate robust, sensitive, and reproducible data generation across eleven international sites on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality.

Suggested Citation

  • Yue Xuan & Nicholas W. Bateman & Sebastien Gallien & Sandra Goetze & Yue Zhou & Pedro Navarro & Mo Hu & Niyati Parikh & Brian L. Hood & Kelly A. Conrads & Christina Loosse & Reta Birhanu Kitata & Sand, 2020. "Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18904-9
    DOI: 10.1038/s41467-020-18904-9
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    Cited by:

    1. Rebekka Wegmann & Ximena Bonilla & Ruben Casanova & Stéphane Chevrier & Ricardo Coelho & Cinzia Esposito & Joanna Ficek-Pascual & Sandra Goetze & Gabriele Gut & Francis Jacob & Andrea Jacobs & Jack Ku, 2024. "Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Mattheus H. E. Wildschut & Julien Mena & Cyril Dördelmann & Marc Oostrum & Benjamin D. Hale & Jens Settelmeier & Yasmin Festl & Veronika Lysenko & Patrick M. Schürch & Alexander Ring & Yannik Severin , 2023. "Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    3. Xiang Liu & Haidan Sun & Xinhang Hou & Jiameng Sun & Min Tang & Yong-Biao Zhang & Yongqian Zhang & Wei Sun & Chao Liu, 2025. "Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    4. Lei Xin & Rui Qiao & Xin Chen & Hieu Tran & Shengying Pan & Sahar Rabinoviz & Haibo Bian & Xianliang He & Brenton Morse & Baozhen Shan & Ming Li, 2022. "A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    5. Huanhuan Gao & Yi Zhu & Dongxue Wang & Zongxiang Nie & He Wang & Guibin Wang & Shuang Liang & Yuting Xie & Yingying Sun & Wenhao Jiang & Zhen Dong & Liqin Qian & Xufei Wang & Mengdi Liang & Min Chen &, 2025. "iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    6. Valdemaras Petrosius & Pedro Aragon-Fernandez & Nil Üresin & Gergo Kovacs & Teeradon Phlairaharn & Benjamin Furtwängler & Jeff Op De Beeck & Sarah L. Skovbakke & Steffen Goletz & Simon Francis Thomsen, 2023. "Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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