Fig. 2

Proteome-wide modulation analysis in severe inflammatory response. a Representation of the LPS/Control ratio for newly synthesized peptides (red columns) and non-newly synthesized peptides (black columns) in the endothelial cells (EC). b Proteins with newly synthesized peptides only detected after LPS challenge in EC. c Representation of the LPS/Control ratio for newly synthesized peptides (red columns) and non-newly synthesized peptides (black columns) in the smooth muscle cells (SMC). d Proteins with newly synthesized peptides only detected after LPS challenge in SMC. Ratios were calculated based on the sum of spectral counts of all SILAM-labeled peptides for newly synthesized proteins and the sum of spectral counts of all non-SILAM-labeled peptides for non-newly synthesized proteins for every protein detected. N.D. refers to not detected. Only proteins with statistical significance assessed by Student’s t test are represented (p < 0.05). Regulation threshold has been set at 1.5 and it is represented with horizontal green dashed lines in every condition. Y-axis for black columns with positive values has been drawn pointing down for visual purposes. e Heatmap of protein turnover detected in EC. Turnover of proteins is expressed as the number of non-tryptic peptides detected in individual proteins expressed in spectral counts. Darker colors refer to lower turnover levels