Measuring pathway database coverage of the phosphoproteome

PeerJ

article

Hannah Huckstep¹  Liam G. Fearnley²  Melissa J. Davis¹ 

[1] Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research;Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne;Division of Population Health, Walter and Eliza Hall Institute of Medical Research;Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne

关键词: Phosphoproteomics;    Databases;    Proteomics;    Bioinformatics;   

DOI  :  10.7717/peerj.11298

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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 seven widely used databases to shed light on their suitability to provide functional insights into phosphoproteomics data. We first determined the global coverage of each database at both the protein and phosphosite level. We also determined how consistent each database was in its phosphorylation annotations compared to a global standard. Finally, we looked in detail at the coverage of each database over six experimental datasets. Our analysis highlights the relative strengths and weaknesses of each database, providing a guide in how each can be best used to identify biological mechanisms in phosphoproteomic data.

【 授权许可】

CC BY