Figure S2. Evaluation of absolute quantitative proteome data of human Ramos B cells.

Related to Fig 2. (A) Protein copy number profile of protein tyrosine phosphatases (PTPs), without the “classical” PTPs shown in Fig 2B, identified in Ramos B cells. (B, C) Scatterplots comparing mean log₁₀ protein copy numbers of naïve B cells (Rieckmann et al, 2017) and Ramos B cells reported in this study. Protein tyrosine kinases present in the dataset are depicted in blue (B) and “classical” PTPs in red (C). (D) Mean log₁₀ copy numbers of the three most abundant “classical” PTPs in naïve B cells compared to Ramos B cells and the difference in expression given as fold-change. (E) Kernel-smoothed distribution curves of RNA sequencing (seq) data of human Ramos B cells calculated from raw data reported in Qian et al (2014). Grey, distribution of transcripts of protein-coding genes; light blue, distribution of transcripts of protein-coding genes with a mean log₂ transcript per million value > 0; dark blue, protein-coding transcripts for which proteins were identified by MS analysis in this work (see Figs 1 and S1 and Table S1). (F) Comparison of log₂-transformed mean transcript per million values and protein copy numbers of ribosomal proteins (purple), proteasome components (red), and enzymes of canonical glycolysis (blue).