Pachysolen translates CUG codons as alanine and not as leucine. (A) Distribution of the mass errors of randomly selected 10% of all peptides (gray dots), 10% of peptides with CUG translated as alanine (red), and 10% of peptides with CUG translated as other amino acids (blue). (B) Proteins identified in the soluble cell extract of Pachysolen sorted by sequence coverage. (C) Number of PSMs covering CUG-codon positions per protein. (D) Percentage of the CUG-codon positions per protein covered by the proteomics data. (E) Number and distribution of observed CUG translations in all peptide spectrum matches from MS/MS analysis. (F) Representative MS/MS spectrum of a peptide containing a CUG translated as alanine. The peptide sequence is shown below the spectrum, with the annotation of the identified matched N-terminal fragment ions (b-type ions) in blue and the C-terminal fragment ions (y-type ions) in red. Only major peaks are labeled for clarity (full annotation of the spectrum is shown in Supplemental Fig. S7).