The technology has gotten better in the form of kits and procedures, and these labels and tags have become useful tools that are much more sensitive than the traditional methods. For protein gels, the use of fluorescent stains is an extension of the use of ethidium bromide as a standard stain for agarose gels. The staining protocols for fluorescent stains are very similar to Coomassie Blue, something most labs are already very familiar with. These stains have sensitivity levels comparable to colloidal Coomassie Blue and some of the rapid silver-staining methods. Fluorescent dyes that do not covalently modify proteins are finding application in the downstream microchemistry that is necessary in proteomics, especially mass spectrometry.
Many factors contribute.
Among these are gel type and concentration, sample preparation, band size, dye concentration, and staining procedures. A good starting point is to always use good raw materials. Run gels with well-separated lanes and strive for good band resolution. Run standards of known quantity or a dilution series, if possible, to produce a standard curve. Bear in mind the linear range of the system.