In order to generate a functional proteome, gene expression pathways must assemble proteins accurately according to the rules of the genetic code. General gene expression accuracy is known to be high, but errors nevertheless occur with measurable frequencies. Here we develop a mass-spectrometry (MS) based assay for the detection of a particular type of gene expression error, amino acid misincorporation. This assay allows assessing a much broader range of misincorporation events compared to current, very sensitive but also very specific enzyme reporter assays. Our assay uncovers a remarkably rich pool of error products for a model protein expressed in E. coli, which depend quantitatively on codon usage in the expression construct. This codon usage dependence can be explained in part as a function of the composition of the tRNA pool in this organism. We further show that codon-dependent differences in error levels correlate with measurable changes in specific protein activity. In contrast to E. coli, error levels are lower, and appear not to be codon usage dependent, when the same model protein is expressed in S. cerevisiae.