The present invention relates generally to instrumentation and methodology for the characterization of chemical samples in solutions or on a surface which is based on modified ionization methods with or without adjustable pH and controllable H-D exchange in solution, in improved ion mobility spectrometer (IMS), a multi-beam ion per-selection of the initial flow, and coordinated mobility and mass ion separation and detection using a single or several independent time-of-flight mass spectrometers for different beams with methods for fragmenting ion mobility-separated ions and multi-channel data recording.