Fig. 6

Two-way clustering of the data sets for SDS-insoluble cytosolic proteins identified by LC-MS/MS from all groups of the mice used in the study. Cluster analysis was performed on the SDS-insoluble peptide spectra data for 191 total proteins identified across all the mice, using the SAINT scoring criteria (Additional file 5, Table S4). These 191 proteins were selected by outer join merging of all the SDS-insoluble proteins from each group. Red is indicative of the highest number of peptide spectra for a given protein whereas blue indicates the lowest number of spectral count for a given protein. The figure was generated by JMP Pro Statistical Discovery from SAS. Note that the number in front of each animal identification represent the run number that produced the LC-MS/MS data. Although there were some small influences of batch in the data clustering, the three main clusters consisted of data sets that were run at very different times in the process