Mass spectrometry-based absolute quantification of single Xenopus embryo proteomes

Abstract

Early Xenopus development is characterized by a poor correlation between global mRNA and protein abundances due to maternal mRNA and protein loading. Therefore, proteome profiling is necessary to study gene expression dynamics during early Xenopus development. In contrast to mammals, single Xenopus eggs and embryos contain enough protein to allow identification and quantification of thousands of proteins using mass spectrometry-based proteomics. In addition to investigating developmental processes, single egg or blastomere proteomes can be used to study cell-to-cell variability at an unprecedented depth. In this protocol, we describe a mass spectrometry-based proteomics approach for the identification and absolute quantification of Xenopus laevis egg or embryo proteomes, including sample preparation, peptide fractionation and separation, and data analysis.