Elemental analysis of individual whole cultured cells using Particle Induced X-ray Emission (PIXE), Scanning Transmission Ion Microscopy (STIM) and Rutherford Backscattering Spectrometry (RBS) can yield quantitative results at the parts per million level. During a continuous scan over a single cell using 2 MeV protons (with a beam current of 100 pA, spot size of 1 μm), elemental loss was monitored and a 60% reduction in hydrogen and oxygen was observed. Concentrations of C, Na, Mg, P, S, Cl, K, Ca, Fe, Cu, and Zn remained constant. The elemental analysis, at the parts per million level, of single whole cultured cells is therefore not limited by beam damage. However, during the irradiation, the size of the cell was observed to shrink by 20%, placing severe restrictions on the imaging and analysis of subcellular structures such as organelles.