Abstract
The oocytes, embryos, and cell-free lysates of the frog Xenopus laevis have emerged as powerful models for quantitative proteomic experiments. In the accompanying paper (Chapter 13) we describe how to prepare samples and acquire multiplexed proteomics spectra from those. As an illustrative example we use a 10-stage developmental time series from the egg to stage 35 (just before hatching). Here, we outline how to convert the ~700,000 acquired mass spectra from this time series into protein expression dynamics for ~9000 proteins. We first outline a preliminary quality-control analysis to discover any errors that occurred during sample preparation. We discuss how peptide and protein identification error rates are controlled, and how peptide and protein species are quantified. Our analysis relies on the freely available MaxQuant proteomics pipeline. Finally, we demonstrate how to start interpreting this large dataset by clustering and gene-set enrichment analysis.
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Acknowledgments
We thank Lillia Ryazanova for help with the sample preparation, and Felix Keber for comments and suggestions on the manuscript. MS was supported by a NIH F31 pre-doctoral fellowship 5F31GM116451. This work was supported by NIH grant 1R35GM128813 and by Princeton University startup funding.
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Sonnett, M., Gupta, M., Nguyen, T., Wühr, M. (2018). Quantitative Proteomics for Xenopus Embryos II, Data Analysis. In: Vleminckx, K. (eds) Xenopus. Methods in Molecular Biology, vol 1865. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8784-9_14
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DOI: https://doi.org/10.1007/978-1-4939-8784-9_14
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