Quantitative Proteomics of Xenopus Embryos I, Sample Preparation

Methods in Molecular Biology
Meera GuptaMartin Wühr

Abstract

Xenopus oocytes and embryos are model systems optimally suited for quantitative proteomics. This is due to the availability of large amount of protein material and the ease of physical manipulation. Furthermore, facile in vitro fertilization provides superbly synchronized embryos for cell cycle and developmental stages. Here, we detail protocols developed over the last few years for sample preparation of multiplexed proteomics with TMT-tags followed by quantitative mass spectrometry analysis using the MultiNotch MS3 approach. In this approach, each condition is barcoded with an isobaric tag at the peptide level. After barcoding, samples are combined and the relative abundance of ~100,000 peptides is quantified on a mass spectrometer. High reproducibility of the sample preparation process prior to peptides being tagged and combined is of upmost importance for obtaining unbiased data. Otherwise, differences in sample handling can inadvertently appear as biological changes. We detail and exemplify the application of our sample workflow on an embryonic time-series of ten developmental stages of Xenopus laevis embryos ranging from the egg to stage 35 (just before hatching). Our accompanying paper (Chapter 14 ) details a bioinformati...Continue Reading

Citations

Jul 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth M HartThomas J Silhavy
Mar 8, 2019·ELife·Blake W TyeL Stirling Churchman
Aug 21, 2021·Molecular Systems Biology·Joseph CrapseMartin Wühr
Dec 12, 2018·Analytical Chemistry·Albert B Arul, Renã A S Robinson
Jun 14, 2019·Analytical Chemistry·Anumita Saha-ShahBenjamin A Garcia
Nov 7, 2019·Journal of Proteome Research·Hyo Jung SimTaejoon Kwon
Sep 25, 2021·Nature Chemical Biology·Wei DaiRalph E Kleiner

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