Figure 1.

Absolute proteomics of the Ciona egg

(A) Schematic of label-free proteomics utilized to determine absolute protein concentrations. Unfertilized Ciona eggs were lysed, and human proteins of known concentrations (UPS2) were added to the lysate as a reference standard. Following normalization as outlined in the materials and methods, we detect ∼195,000 peptides and estimate protein concentrations for ∼6,000 proteins.

(B) Table of selected proteins in the unfertilized egg including the top 5 most abundant and some transcription factors important to embryonic development.

(C) Histogram of all quantified proteins in the Ciona egg (gray) with superimposed kernel density estimates (KDE) of transcription factors (TFs - red) and signaling molecules (SMs - blue). Both TFs and SMs follow a distribution similar to the global egg proteome (black) but with a lower median concentration. The complete data is provided in Table S1.

(D) Stoichiometries of protein complexes. Concentrations of subunits from a shared protein complex display comparable values and show typically a statistically different distribution than the entire proteome (∗p < 0.01, two-way ANOVA with Tukey’s multiple-comparisons test).