|In nanomechanical mass spectrometry, the signal due to a molecule depends not only on the mass of the molecule, but also the landing position of the molecule on the mechanical beam. Hence, there is a need to decouple the mass information from the position-dependency for each measured molecule. Here, we present a method to extract out the mass information by using two different vibration modes of a nanomechanical resonator. We show multimode frequency tracking data for gold nanoparticle and biomolecule samples, introduced by electrospray ionization and RF hexapole based ion guidance. Resulting frequency jumps of the mechanical device are converted into mass and position information.