Journal article
Strategies to enable large-scale proteomics for reproducible research
RC Poulos, PG Hains, R Shah, N Lucas, D Xavier, SS Manda, A Anees, JMS Koh, S Mahboob, M Wittman, SG Williams, EK Sykes, M Hecker, M Dausmann, MA Wouters, K Ashman, J Yang, PJ Wild, A deFazio, RL Balleine Show all
Nature Communications | Published : 2020
Abstract
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 biol..
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Awarded by University of Sydney
Funding Acknowledgements
Ovarian cancer tissue was accessed from the Gynaecological Oncology Biobank (GynBiobank) Western Sydney Local Health District, Westmead. GynBiobank is a member of the Australasian Biospecimen Network-Oncology group funded by National Health and Medical Research Council (NHMRC) of Australia Enabling Grants 310670 and 628903 and Cancer Institute New South Wales (NSW) Grants 12/RIG/1-17 and 15/RIG/1-16. Assistance from Dr Maiken Marcker Espersen of the Westmead Institute for Medical Research and Catherine Kennedy of GynBiobank is gratefully acknowledged. Prostate cancer tissue was accessed from University Hospital Zurich, Switzerland. Assistance from Dr Christian D. Fankhauser (University Hospital Basel), Dr Thomas Hermanns, Dr Cedric Poyet and Dr Niels J. Rupp (University Hospital Zurich) is gratefully acknowledged. The provision of yeast by Prof Marc Wilkins of the University of New South Wales is gratefully acknowledged. ProCan (R) is supported by the Australian Cancer Research Foundation, Cancer Institute NSW (2017/TPG001, REG171150), NSW Ministry of Health (CMP-01), University of Sydney, Cancer Council NSW (IG 18-01), Ian Potter Foundation, the Medical Research Futures Fund (MRFF-PD), NHMRC of Australia (GNT1170739), and National Breast Cancer Foundation (IIRS-18-164). R.C.P. and P.J.R. are supported by NHMRC Fellowships (GNT1138536 and GNT1137064, respectively).