T. brucei proteome coverage using SILAC and mass spectrometry. Comparison of mass spectrometry and genome encoded proteome. (A) molecular weight, (B) isoelectric point and (C) transmembrane domains. Histograms depict the number of proteins of a certain class encoded in the genome (blue) and detected by mass spectrometry (red). The insets depict a density plot of the corresponding histogram indicating which regions are over/under represented when comparing genome and mass spectrometry. (D) Distribution of protein ratios from the three life stages of T. brucei across the 11 mega-chromosomes. From outside to inside, the chromosomes one to 11, the polycistronic transcription units (PTUs) on the chromosomes (red, PTU on sense strand; blue, PTU on antisense strand), protein ratios LS/PC, SS/LS, PC/SS (green, ≥ 2x up; red, ≥ 2x down; black unchanged).