A hybrid mass spectrometer comprising: an ion source for generating ions from a sample, a first mass spectral system comprising a nanoelectromechanical mass spectral (NEMS-MS) system, a second mass spectral system including at least one mass analyzer adapted to separate the charged particles according to their mass-to-charge ratios, and an integration zone coupling the first and second mass spectral systems, the integration zone including at least one directional device for controllably routing the ions to a selected one or both of the first and second mass spectral systems for analysis thereby. The second system can be an orbital electrostatic trap system. The ion beam can be electrically directed to one or the other system by ion optics. A chip with resonators can be used with cooling. Uses include analysis of large mass complexes found in biological systems, native single molecule analysis, and size and shape analysis.