Abstract
Global phosphoproteomics investigations yield overwhelming datasets with up to tens of thousands of quantified phosphosites. The main challenge after acquiring such large-scale data is to extract the biological meaning and relate this to the experimental question at hand. Systems level analysis provides the best means for extracting functional insights from such types of datasets, and this has primed a rapid development of bioinformatics tools and resources over the last decade. Many of these tools are specialized databases that can be mined for annotation and pathway enrichment, whereas others provide a platform to generate functional protein networks and explore the relations between proteins of interest. The use of these tools requires careful consideration with regard to the input data, and the interpretation demands a critical approach. This chapter provides a summary of the most appropriate tools for systems analysis of phosphoproteomics datasets, and the considerations that are critical for acquiring meaningful output.
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Acknowledgments
The authors would like to thank members of the Proteomics Program at the Novo Nordisk Foundation Center for Protein Research (CPR) for critical input on the protocol. Work at CPR is funded in part by a generous donation from the Novo Nordisk Foundation (Grant number NNF14CC0001).
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Munk, S., Refsgaard, J.C., Olsen, J.V. (2016). Systems Analysis for Interpretation of Phosphoproteomics Data. In: von Stechow, L. (eds) Phospho-Proteomics. Methods in Molecular Biology, vol 1355. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-3049-4_23
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