Extended Data Fig. 8: Quantitative comparison of core-subunits, substrates, adaptors and unclassified proteins coeluting with CCT/TRiC-PFD and PFD complexes in the PFDN2 and UXT DIP-MS experiments.
From: DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes
a. Recovery of CCT/TRiC-PFD and PFD subunits in the DIP-MS experiments of PFDN2 and UXT. b. Boxplot of the log10quantitative protein abundance of core-subunits (max. MS2 signal at the CCT/TRiC-PFD or PFD peaks) in the PFDN2 (n = 3 biologically independent experiments) and UXT DIP-MS (n = 3 biologically independent experiments) experiments. The low abundance of canonical PFD complex in the UXT DIP-MS, indicates that the PFD complex is a background contaminant within this experiment. The solid line represents the median, box limits show the IQR and its whiskers 1.5 x IQR. The dots show the mean signal across DIP-MS replicates for each core-subunit at the coelution peak. The number of dots varies due to missing values. c. Boxplot of log2FC of core-subunits quantified in the PFDN2 DIP-MS (n = 3 biologically independent experiments) against UXT DIP-MS (n = 3 biologically independent experiments) on protein abundance level. The solid line represents the median, box limits show the IQR and its whiskers 1.5 x IQR. Dots represent the mean log2FC across all DIP-MS replicates for each core-subunit split by coelution group (CCT/TRiC-PFD: n = 15, and PFD n = 6). d. Recovery of CCT/TRiC-PFD and PFD coeluting proteins in the DIP-MS experiments of PFDN2 and UXT. e. Boxplot of log10 quantitative protein abundance of coeluting proteins (max. MS2 signal at the CCT/TRiC-PFD or PFD peaks) in the PFDN2 (n = 3 biologically independent experiments) and UXT DIP-MS experiments (n = 3 biologically independent experiments). The solid line represents the median, box limits show the IQR and its whiskers 1.5 x IQR. The dots show the mean signal across DIP-MS replicates for each protein at the coelution peak. The number of dots varies due to missing values. f. Boxplot of log2FC of coeluting proteins quantified in the PFDN2 DIP-MS (n = 3 biologically independent experiments) against UXT DIP-MS (n = 3 biologically independent experiments) on protein abundance level. The solid line represents the median, box limits show the IQR and its whiskers 1.5 x IQR. Dots represent the mean log2FC across all DIP-MS replicates for each coeluting protein split by coelution group (CCT/TRiC-PFD: n = 32, and PFD n = 21 coeluting proteins).
