Figure 1.

SCCP workflow. The workflow developed for SCCP included cell culturing and treatment with drugs, isolation of individual cells by FACS, protein extraction and digestion, TMT labeling of thus obtained tryptic peptides followed by multiplexing, LC-MS/MS, and statistical data analysis. All steps are optimized for achieving the desired proteome depth and quantitative correlation with bulk analysis. In the figure, the split carrier proteome occupies two channels (131N and 131C) in a TMT11plex set, with two other channels (130N and 130C) remaining empty (dotted lines). Identification of peptides is achieved via matching masses of sequence-specific fragments, and quantification is performed by the abundances of the low-mass TMT reporter ions.