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

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, Sander R. Piersma, Davide Chiasserini, Hongwen Zhu, Guixue Hou, Muhammad Tahir, Andrew Macklin, Amanda Khoo, Xiuxuan Sun, Ben Crossett, Albert Sickmann, Yu-Ju Chen, Connie R. Jimenez, Hu Zhou, Siqi Liu, Martin R. Larsen, Thomas Kislinger, Zhinan Chen, Benjamin L. Parker, Stuart J. Cordwell, Bernd Wollscheid () and Thomas P. Conrads ()
Additional contact information
Yue Xuan: Thermo Fisher Scientific GmbH
Nicholas W. Bateman: Uniformed Services University and Walter Reed National Military Medical Center
Sebastien Gallien: Thermo Fisher Scientific
Sandra Goetze: Institute of Translational Medicine, Department of Health Sciences and Technology
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
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
Ben Crossett: The University of Sydney
Albert Sickmann: Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V.
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
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
Thomas P. Conrads: Women’s Service Line, Inova Health System

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-18904-9

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