Fig. 6.

Global analysis of cleaved substrates. A, calculation of a background population for enrichment testing. To perform unbiased enrichment testing of cleavage substrates versus the whole proteome, a background population was extracted from the whole proteome data spanning intensity ranges equal to those of the substrate population. All three categories are depicted. B, enrichment analysis of substrates. Proteins in complexes are slightly enriched within the substrate population. Proteins assigned to mitochondrion are significantly de-enriched within the substrate population. Bg, background. C, distribution of uncleaved ratios of all substrates. Median ratios of the uncleaved protein regions follow a clear bimodal distribution in all experiments. D, representation of uncleaved protein ratios with regard to proteins in complexes. Substrates annotated in CORUM showed clear tendencies toward the right-hand peak; substrates not assigned to complexes tended toward stronger negative ratios.