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Phenotypically distinct populations of cells can be produced by fluorescence-activated cell sorting (FACS) and the global protein differences between the populations can be investigated by the techniques of proteomics, including nanoflow LC/ MSn. In our initial studies, we have examined the combined use of FACS to produce highly purified populations of CD4+ and CD8+ T-cells with long-gradient nanoflow LC/MSn to analyze the peptides released from those cell surface proteins that are susceptible to cleavage by trypsin.
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