Abstract
While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.
Highlights
Recent technological developments have enabled single cell studies at the level of genomics, transcriptomics, proteomics and metabolomics [1,2]
Mass spectrometry-based proteomics emerged as a powerful tool to study the cellular proteome in an unbiased and comprehensive manner [13,14]
In order to distinguish technical variation from biological noise, a cell lysate from a single egg was split into three and handled separately. This was done for three individual eggs from the same mother and all nine samples were prepared for mass spectrometry using filter-aided sample preparation (FASP) (Figure 1A) [30]
Summary
Recent technological developments have enabled single cell studies at the level of genomics, transcriptomics, proteomics and metabolomics [1,2]. Generation sequencing technology allows unbiased and comprehensive sequencing of RNA from single cells [3,4,5] These pioneering studies have revealed cellular heterogeneity and stochastic gene expression at the single-cell level, which are overseen in analyses on cell populations. Mass cytometry emerged as a novel technology to study the absolute abundance of proteins in single cells without the need to tag proteins but using endogenous antibodies to which heavy metals are coupled. This method currently allows quantifying up to 32 cellular proteins at the single-cell level in a single experiment [11,12]. Examples include oocytes or eggs which are several orders of magnitude larger than somatic cells
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
