There are a number of applications for flow cytometry, including, but not limited to: 

Immunophenotyping- Using fluorescence-conjugated antibodies directed toward a protein(s) of interest, cells expressing that protein(s) on the surface or intracellularly may be detected by flow cytometry.  Specific cell types may be distinguished within a mixed population using multiple fluorescence-conjugated antibodies. 

Transfection efficiency may be determined when a fluorescent protein (i.e. GFP) is used as a marker. 

Apoptosis measurement- Several flow cytometric methods to detect apoptosis are available. 

Cell cycle analysis- Fixed cells are stained with a dye that binds to DNA (e.g. propidium iodide).  Fluorescent intensity is used to determine the amount of cellular DNA present in each cell (i.e. two copies of a genome have roughly twice the fluorescent intensity of one copy). 

Cell proliferation- Carboxyfluorescein diacetate, succinimidyl ester (CFSE) is a dye that diffuses into cells and is passed from parent to daughter cells so that the cells of each generation have half the fluorescent intensity of their parent cells. 

Cell sorting- A particular subset(s) of cells may be sorted from a mixture of cells based upon particular properties.  Currently we have a Miltenyi magnetic sorter, with a Flow sorter joining the line up soon. 

Membrane potential- Bacterial membrane potential may be analyzed using DiOC₂, which exhibits green fluorescence in all bacterial cells, but shifts to red fluorescence as the dye becomes more concentrated in cells with larger membrane potentials.  Mitochondrial membrane potential may be analyzed in the same manner with JC-1. 

Cytometric Bead Arrays- CBAs allow the detection of specific soluble proteins from serum, cell culture supernatant, or cell lysates.  The CBA Flex Sets provide the flexibility of choosing from 1 to 72 different soluble proteins for analysis from a wider range of species.