Strategies to enable large-scale proteomics for reproducible research.

Autor: Poulos RC; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Hains PG; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Shah R; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Lucas N; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Xavier D; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Manda SS; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Anees A; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Koh JMS; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Mahboob S; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Wittman M; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Williams SG; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Sykes EK; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Hecker M; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Dausmann M; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Wouters MA; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Ashman K; Sciex, 2 Gilda Court, Mulgrave, VIC, Australia., Yang J; School of Mathematics and Statistics, The University of Sydney, Sydney, Australia., Wild PJ; Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany.; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland., deFazio A; Centre for Cancer Research, Westmead Institute for Medical Research, Westmead, NSW, Australia.; Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia.; Department of Gynaecological Oncology, Westmead Hospital, Westmead, NSW, Australia., Balleine RL; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Tully B; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Aebersold R; Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.; Faculty of Science, University of Zürich, Zürich, Switzerland., Speed TP; Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia., Liu Y; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.; Yale Cancer Biology Institute, Yale University, West Haven, CT, USA., Reddel RR; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Robinson PJ; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia., Zhong Q; ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia. qzhong@cmri.org.au.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2020 Jul 30; Vol. 11 (1), pp. 3793. Date of Electronic Publication: 2020 Jul 30.
DOI: 10.1038/s41467-020-17641-3
Abstrakt: Reproducible research is the bedrock of experimental science. To enable the deployment of large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time and across instruments and develop computational methods for improving quantitative accuracy. We perform 1560 data independent acquisition (DIA)-MS runs of eight samples containing known proportions of ovarian and prostate cancer tissue and yeast, or control HEK293T cells. Replicates are run on six mass spectrometers operating continuously with varying maintenance schedules over four months, interspersed with ~5000 other runs. We utilise negative controls and replicates to remove unwanted variation and enhance biological signal, outperforming existing methods. We also design a method for reducing missing values. Integrating these computational modules into a pipeline (ProNorM), we mitigate variation among instruments over time and accurately predict tissue proportions. We demonstrate how to improve the quantitative analysis of large-scale DIA-MS data, providing a pathway toward clinical proteomics.
Databáze: MEDLINE