Figure 3. Accurate quantification of protein changes by SILAC.

Relative changes in protein abundance after 90 min of singlet oxygen stress were determined by an indirect quantification approach using a heavy standard labeled with ¹³C₆-lysine (Lys6). Protein mixtures were digested and used for MS analysis (see Materials and Methods). In the central volcano plot the direct ratios (log₂) of 1214 quantified proteins of quadruplicates were plotted against negative logarithmized p-values (log₁₀). The histogram on the top shows log₂ protein ratio distributions (Gaussian distribution). Up- and down-regulated proteins were grouped according to their functions which relate to stress defense (red triangles), proteases (black triangles), redox reactions (dark blue triangles), carbohydrate metabolism (grey triangles), transport processes (light blue triangles), photosynthesis (green triangles), and motility/chemotaxis (purple triangles). See supplementary Table S3 for further information on regulated proteins and their particular functions.