Quenching refers to any process, which decreases the Fluorescence intensity of Fluorophores. A variety of processes can result in quenching, such as excited state reactions, energy transfer, complex-formation, and collisional quenching. 

Ligand-induced quenching, affecting the Initial Fluorescence intensity can be a direct measure for an interaction, either caused by conformational changes of the Target molecule or binding of a Ligand in proximity to the fluorophore. However, if ligand-dependent quenching occurs that exceeds the general limit of - 20%, an inner filter effect, protein loss due to adsorption to labware or aggregation/precipitation must be excluded by control experiments, listed under Ligand-Induced Fluorescence Change.