Fig. 6.

Quantitative N-terminome analysis in FTSH12 mutants compared with wild type. (A) Positional annotation of 1292 identified N-terminal peptides. Peptides mapping to translation start sites with intact or excised initiator-Met (Pos1/2) or within five amino acids of TargetP2.0 annotated as signal peptide, plastid or mitochondrial transit peptide or propeptide maturation sites, were defined as ‘expected’ N termini. Light grey, peptides with endogenous N-terminal acetylation; dark grey, peptides in vitro marked by dimethylation, indicating in vivo free N-terminal amines. (B) Volcano plots of N-terminal peptide abundance in ox12-1 compared with mi12-3. Peptides from plastid-located proteins (plastid encoded or predicted to target to the plastid by TargetP2.0) are highlighted in green. N-terminal peptides with significantly reduced or increased abundance (Student´s t-test P-value<0.05 and log₂ FC<–0.58 or >0.58) are highlighted with blue and red color background. (C) Comparison of N-terminal peptide abundance with the corresponding protein abundance within ox12-1 and mi12-3. Peptides from plastid proteins are highlighted in green. Pearson correlation coefficient with confidence level is indicated. (D) Comparison of the position of plastid protein N-terminal peptides to the transit peptide cleavage predicted by TargetP2.0. Protein termini showing significant accumulation or depletion change in ox12-1 compared with mi12-3 are highlighted in red and blue, respectively. Dark grey indicates unaltered abundance, light grey indicates peptides not quantified in two or more replicates.