Overview of proteomic and transcriptomic data. (A) Scatter plots examining the reproducibility of the iTRAQ quantitation procedure on stem cells. Top and middle panels show plotted ratios from proteins using the internal duplicates LSK^–/LSK^– and LSK⁺/LSK⁺, respectively, from one experiment. No ratios are seen greater than 1.2-fold, giving confidence in the cut-off value chosen. The bottom panel shows plotted ratios from proteins for one of the LSK^–/LSK⁺ datasets, clearly demonstrating differences in the protein expression profiles between the 2 cell types. (B,C) Expression profiles of LSK^– cells versus LSK⁺ cells. Panel B shows fold changes in 704 proteins in rank order between LSK^– and LSK⁺ cells alongside corresponding expression ratios for transcripts of these proteins obtained by microarray analysis. Panel C shows the same expression data, sorted in rank order of fold change in the mRNA level, alongside corresponding protein expression ratios.