Forward Scatter (FSC, FS, FALS, etc.) This parameter is a rough indicator of a cell's size.
Side Scatter (SSC, SS, RT. ANG., 90, etc.) This parameter is a rough indicator of cellular granularity, membrane complexity, number of organelles, etc.
Taken together, the two scatter parameters give a morphological fingerprint of whatever is flowing through the cytometer. In addition to the intact, non-aggregated cells that are present in cell suspensions, there are a variety of other particles, including cells debris (smaller) and clumps (larger). Although it is possible to "gate" flow cytometry data based on scatter parameters, this is no substitute for preparative steps that minimize fragmentation and clumping.
Immunofluorescence: proteins are detected with antibodies that have been conjugated to fluorescent molecules such as FITC, PE, Texas Red, APC, etc. Detection of molecules on the cell surface (immunophenotyping) is most common, but with a few modifications, proteins can be identified in the cytoplasm (e.g. cytokines), or in the nucleus (e.g. cell cycle control proteins).
Cell cycle/proliferation: DNA content can be measured with PI, 7-AAD, the Hoechst dyes, or DAPI. BrdU incorporation for cell proliferation can be measured by immunofluorescence. This is often done along with DNA staining.
Apoptosis can be measured in a number of ways. The TUNEL technique identifies DNA strand breaks. Annexin V labeling detects changes in the plasma membrane asymmetry. Nuclear condensation and DNA loss are demonstrated by hypodiploid peaks in DNA content experiments. Uptake of Hoechst 33258 has also been shown to increase with apoptotic changes.
Mitochondrial function (Rh123, DiOC6)
Oxidative burst (HE, DCFH-DA, DHR)
Reporter genes (GFP, LacZ, along with the substrate FDG)
Glutathione/reductive reserve (MCB)
Ca++ flux (Indo-1)
Enzyme activity (fluorescent substrates)
Tracking of cell division and conjugation (fluoroscein, calcein, PKH26)
Total protein content (SR101, fluoroscein)