Figure 4

SRM analysis confirms differential expression of proteins between TGCV patient and control cells. (A) Seven of top 10 over-expressed proteins were successfully quantified in SRM analysis, showing the same trend as in SILAC proteomic analysis. (B) Seven of top 10 under-expressed proteins were successfully quantified. These proteins showed the same trend as in SILAC proteomic analysis, except for one protein. Y-axis indicates the peak area ratio of the endogenous peptide to SI-peptide. Protein names and target peptide sequences for SRM are indicated at the top of each graph. Symbols represent each cell used in SRM analysis, as described in the figure. (C and D) Examples of peak groups of each peptide transition obtained in SRM analysis. The peak areas from each chromatogram are displayed in parallel and represent detected ion intensities. Colors indicate the different transitions of each peptide. (C) CTHRC1: Three endogenous target peptides were quantified. (D) PLIN2: Two endogenous target peptides were quantified (left and middle panels). One peptide was not quantified due to a low signal-to-noise ratio in control1 (right panel). Target peptide sequences are indicated at the top. Characters at the bottom indicate cell names. Analyses were run in duplicate.