Figure 3. Differential expression analysis reveals biomarkers of mitochondrial disease.

Volcano representation of differentially expressed (DE) proteins in groups versus controls in (A) Mitochondrial disease patients (MitoPatients); (B) CI; (C) MtProt; (D) MtGenExp; (E) MtARS; (F) CIV. Significantly changed proteins (Log₂FC > 1.3 or Log₂FC < –1.3, adj. P < 0.05) are shown in red (increased) and blue (decreased). P values were adjusted with Benjamini-Hochberg method and are presented in –Log₁₀ scale (–Log₁₀ adjusted P). (G) Heatmap of curated DE proteins, identified in at least 1 of the above comparisons, colored by Log₂ fold-change versus average control (Log₂FC) and further annotated with (+) if significantly differentially expressed (adj. P < 0.05) in the specific comparison. (H) Boxplot of DE proteins of interest, obtained from parallel reaction monitoring mass spectrometry (targeted proteomics) in pooled control (C1–C3) and patient samples (P1–P3). C/P1–C/P3 number indicates technical replicate. Ratios between endogenous peptides (light) and spiked isotope labeled standards (heavy) were determined, normalized to the mean of the control values and Log₂ transformed (Log₂ L/H Ratio).