1. A system for analyzing and imaging a sample containing molecules of interest, the system having: (A) an atmospheric-pressure or near-atmospheric-pressure ionization region; (B) a sample holder for holding the sample, the sample holder being disposed within said ionization region, the sample comprising an analyte embedded in an ionization-assisting matrix chosen such that said matrix facilitates ionization of said analyte to form analyte ions upon light-induced release of said analyte from said sample; (C) a laser for near field illumination of said sample, to induce said release of said analyte from said sample, and to induce ionization of said analyte to form said analyte ions; (D) a mass spectrometer having at least one evacuated vacuum chamber; (E) an atmospheric pressure interface connecting said ionization region and said mass spectrometer (a) for capturing said analyte ions and neutrals released from said sample, (b) for subjecting the neutrals to additional ionization or post ionization, and (c) for transporting said analyte ions to said spectrometer; (F) a scanning near-field optical microscopy instrument comprising (a) a near-field apertureless probe in which said laser is focused onto a sharp metal or metalized tip for scanning the sample; (b) a vacuum capillary nozzle with heating for sucking in particles which are desorbed by said laser, the nozzle being connected to an inlet orifice of said atmospheric pressure interface; (c) a scanner platform connected to the sample holder, the platform being movable to a distance within a near-field distance of the probe; and (d) a controller for maintaining distance information about a distance between said probe and said sample, to thereby hold said sample within said distance; wherein an output of said probe has a spot size on said sample roughly equal to the output diameter of said probe; (G) a recording device for recording topography and mass spectra made during scanning of the sample with the near-field probe; (H) a plotting device for plotting said topography and mass spectrum measurements as separate x-y mappings; and (I) an imaging device for providing images of the x-y mappings.