Figure 2

Distribution of the labeled proteins across time points. (A), Venn diagram summarizing the number of labeled proteins in the total identifications (labeled + unlabeled). The total 2202 proteins identified in this study are the leucine containing proteins only. (B), Distribution of the labeled proteins over the time course analysis. The numbers on the top of each bar show the total proteins (labeled + unlabeled), the green bars show the labeled proteins and the orange bars show proteins without labels. (C), Heatmap showing the changes in the abundances of the labeled proteins over time. The observed heavy (H) and light (L) peptide intensities were used to calculate RIA [I_H/(I_H+I_L)], which were then exported to DanTE [59] for log₂ based normalization and rolling into proteins using Reference Peptide based scaling (RRollup). The normalized RIA values were used for hierarchical clustering into the heatmap. (D), Functional classification of the labeled proteins based on KEGG pathway [27] and Gene Ontology (GO) analysis. The RIA for each category was calculated as an average of all the proteins belonging to each category across all time-course. The log2 transformed RIA values of all the labeled proteins can be found in Additional file 1, Table S2. The list of labeled peptides with their actual RIA is provided in the Additional file 1, Table S2.