Mechanical resonators realized on the nanoscale by now offer applications in mass sensing of bio-molecules with extraordinary sensitivity. The general idea is that perfect mechanical mass sensors should be of extremely small size to achieve zepto- or yocto-gram sensitivity in weighing single molecules similar to a classical scale. However, the small effective size and long response time for weighing biomolecules with a cantilever restricts their usefulness as a high-throughput method. Commercial mass spectrometry (MS) on the other hand, such as electro-spray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-MS and their charge amplifying detectors are the gold standards to which nanomechanical resonators have to live up to. These two methods rely on the ionization and acceleration of biomolecules and the following ion detection after a mass selection step, such as time-of-flight (TOF). Hence, mass spectra are typically represented in m/z, i.e. the mass m to ionization charge ratio z. The principle we are describing here for ion detection is based on conversion of kinetic energy of the biomolecules into thermal excitation of CVD diamond nanomembranes via phonons, followed by phonon-mediated detection via field emission of thermally emitted electrons. We fabricated ultrathin diamond membranes with extreme aspect ratios for MALDI-TOF MS of high mass proteins. These diamond membranes are realized by straightforward etching methods based on semiconductor processing. Ion detection is demonstrated in MALDI-TOF analysis over a broad range of proteins from Insulin to BSA. The resulting data and numerical calculations for detection with diamond nanomembranes offer the better sensitivity and overall performance in resolving protein masses as compared to existing detectors.