RNA-seq-based HVC gene expression correlated with HVC protein SWATH-MS results. The data were normalized to the expression levels of the ENT; positive values indicate higher expression in HVC. For 10 of the 13 investigated proteins, the correlation between protein and mRNA abundance is strong (r = 0.76). Nonetheless, we also found examples where the post-translational control of gene expression appears to be crucial: the endophilin SH3GL2 had a substantially higher protein expression level (as predicted from its RNA level), whereas levels of the calcium-transporting ATPase ATP2B1were lower than its mRNA expression would indicate. The insert shows an exemplary peptide chromatogram from SWATH-MS  for the peptide ASDPAAPPEEAK, which is specific for the protein MBP and is less expressed in the ENT compared with the HVC. Y-axis: intensity cps × 103.