Analysis of Genetic Code Ambiguity Arising from Nematode-Specific Misacylated tRNAs
(A) Summary of the whole-cell proteome analysis of mixed-stage C. elegans. Values are the unique peptide counts at each step. Values in parentheses are the count of candidate peptides containing misincorporated Ser at the Gly (GGG) codon (negative control). (B) Boxplot of the confidence scores for the candidate peptides in Step 2. Significant differences were determined with Student’s two-sided t test. (C) Example of the validation of targeted proteomics. Extracted ion chromatograms of the candidate peptide and the synthetic peptide SPASLDDDIK (an internal standard) are shown. The candidate peptide ion was separated > 1.0 min earlier than the internal standard, indicating that the amino acid sequence of the candidate peptide was inconsistent with the sequence SPASLDDDIK.