Journal article

Measuring pathway database coverage of the phosphoproteome

Hannah Huckstep, Liam G Fearnley, Melissa J Davis

PEERJ | PEERJ INC | Published : 2021

Abstract

Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. There has been finite success in using data-driven approaches to reveal phosphosite functionality due to a range of limitations. The alternate, more suitable approach is making use of prior knowledge from literature-derived databases. Here, we analysed seve..

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University of Melbourne Researchers

Grants

Awarded by National Health and Medical Research Council


Awarded by Cancer Council Victoria fund


Awarded by Cure Brain Cancer Foundation


Funding Acknowledgements

This work was supported by the National Health and Medical Research Council funding (Project Grant 1128609 to Melissa J. Davis), Cancer Council Victoria funding (Project grant 1187825 to MJD), and the National Breast Cancer Foundation and Cure Brain Cancer Foundation funding (Project Grant CBCNBCF-19-009 to MJD). Melissa J. Davis is the recipient of the Betty Smyth Centenary Fellowship in Bioinformatics. HAH was supported by the Peter Hall Scholarship. This study was made possible through Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support scheme. Liam G. Fearnley was supported by the DHB Foundation Centenary Postdoctoral Fellowship in Neurogenetic Systems Biology and philanthropic funding provided through the Walter and Eliza Hall Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.