We find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article.
One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files.
Note to self: look into open-source software and standard data formats for proteomic data.