Advancing Mass Spectrometry-Based Large-Cohort Proteomics for Precision Medicine – An International Cancer Moonshot Multi-Site Study

[Orbitrap_SciLib]

Yue Xuan1, 2, N.W. Bateman3 , S.Gallien2,14, Y. Zhou15, N. Parikh3 , M. Hu15, P. Navarro1 , Y. Chen4 , A. Sickmann5 , B. Wollscheid6 , C.R. Jimenez7 , M.R. Larsen8 , H. Zhou9 , S. Liu10 , Z. Chen11 , T. Kislinger 12 , B. Crossett 13 , B. Hood3 , R. Birhanu Kitata 4 , C. Lorenz 5 , C. Loosse 5 , S. Goetze 6 , S. Piersma 7 , D. Chiasserini 7 , M. Tahir 8 , H. Zhu9 , G. Hou10 , X. Sun11 , A. Macklin12 , A. Khoo12 , B. L. Parker 16 , S. J. Cordwell 16 , Thomas. P. Conrads 3,17
ASMS 2018
Purpose: A high-throughput and reproducible proteome profiling workflow for a large-cohort study was benchmarked across multiple Cancer Moonshot sites worldwide utilizing identical instrument platforms, procedures, and software, and demonstrated to be stable in a 24/7 operation mode for seven consecutive days. Methods: Experiments were performed using capillary chromatographic separation with a one-hour gradient online coupled to a mass spectrometer implementing a high resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) mode. Results: With the one-hour capillary LC-HRMS1 DIA workflow, ~ 7100 to ~8500 protein groups are identified, > 6000 proteins are quantified in average. > 80% protein groups were identified and quantified in common across all the laboratories, and > 80% were identified and quantified in common across different days at the same site


1) Thermo Fisher Scientific (Bremen) GmbH 2) Thermo Fisher Precision Medicine Science Center, Cambridge, MA , USA 3) Gynecologic Cancer Center of Excellence, Murtha Cancer Center, Uniformed Services University of the Health Sciences, MD, USA 4) Institute of Chemistry, Academia Sinica, Taipei, Taiwan 5) Leibniz-Institut für Analytische Wissenschaften — ISAS —“ e.V., Dortmund, Germany 6) Institute of Molecular Systems Biology,Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland 7) Dept. Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, Netherlands 😎 Dept. Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark 9) Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 10) BGI-SHENZHEN, Beishan Road, Shenzhen, China 11) Cell Engineering Research Center / National Key Discipline of Cell Biology, The Fourth Military Medical University, Xi'an City, China 12) Princess Margaret Cancer Centre, Toronto, Canada 13) Sydney Mass Spectrometry, The University of Sydney, Australia 14) Thermo Fisher Scientific, Paris, France; 15) Thermo Fisher Scientific (China) Co. Ltd, Shanghai, China 16) School of Life and Environmental Science, The University of Sydney, Australia 17) The Inova Schar Cancer Institute, VA, USA