The detection and quantitation of individual proteins is one of the fundamental aspects of proteomics. Immunological-based methods such as quantitative enzyme-linked immunosorbent assays (ELISA), Western blotting and dot blotting are very common and sensitive assays for protein detection, and they use antibodies that react specifically with entire proteins or specific epitopes (e.g., fusion tags) after cell lysis. Detection techniques are typically based on chemiluminescence or fluorescence.
For live-cell detection of proteins, fluorescence imaging microscopy is now routinely used. The most common and conventional method is the use of intrinsically fluorescent proteins (FPs) related in structure or sequence to green fluorescent protein (GFP). Alternatively, a series of self-labeling enzymes have been developed that can covalently attach a fluorescent ligand to one of its own amino acid residues. These enzymes are similar in size to FPs. If these enzyme domains are fused in frame to a protein, the pair can be labeled by introducing a cell-permeable fluorescent ligand, which covalently reacts with the fusion tag.