Figure 4: Influence of 3′ UTR shortening on protein levels in murine T cells.

(a) Quantitative mass spectrometry (liquid chromatography-mass spectrometry (LC-MS))-based proteomics workflow. Proteins extracted from naive and activated mouse and human T cells were digested and subjected to label-free and tandem mass tag (TMT) quantification, respectively. The TMT-labelled peptides were further fractionated using isoelectric focusing before LC-MS analysis to increase proteome coverage. Finally, the ratios obtained by the TMT approach were correlated with the label-free quantities to correct for possible ratio distortion effects in the final TMT-based quantitative data sets, which comprised more proteins than the data sets based on LFQ. (b) Correlation of mRNA and protein abundance changes between activated and naive T cells. (c) Change in protein abundance between activated and naive T cells for genes with one to four or more tandem poly(A) sites. (d) Correlation between the change in proximal poly(A) site use and the change in protein level.