We discuss modern developments in quantum optics with organic molecules, clusters and nanoparticles — in particular recent realizations of near-field matter wave interferometry. A unified theoretical description in phase space allows us to describe quantum interferometry in position space and in the time domain on an equal footing. In order to establish matter wave interferometers as a universal tool, which can accept and address a variety of nanoparticles, we elaborate on new quantum optical elements, such as diffraction gratings made of matter and light, as well as their absorptive and dispersive interaction with complex materials. We present Talbot-Lau interferometry (TLI), the Kapitza-Dirac-Talbot-Lau interferometer (KDTLI) and interferometry with pulsed optical ionization gratings (OTIMA) as the most advanced devices to study the quantum wave nature of composite matter. These experiments define the current mass and complexity record in interferometric explorations of quantum macroscopicity and they open new avenues to quantum-assisted metrology with applications in physical chemistry and biomolecular physics.