A complete cold chain freeze-fracture methodology has been developed to test the feasibility of using time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging for the molecular analysis of frozen hydrated biological samples. Because the technique only samples the first few monolayers of a sample, water on the surface of a sample can be a major source of interference. This problem can be minimized by placing a cold trap (fracture knife and housing at -196 degrees C) near the fractured sample that is held at a warmer temperature (-97 to -113 degrees C). This results in removal of surface water and prevents condensation on the surface. Although this approach is effective, it has been found that sample warming needs to be carefully controlled due to the volatility of other matrix molecules and the morphological effects imparted onto the cell surface during drying. By utilizing the above handling technique, it has been possible to demonstrate for the first time that TOF-SIMS imaging technology can be used to obtain images of molecular species across a cell surface with a submicrometer ion probe beam. Images of small hydrocarbons and the deliberately added dopants DMSO and cocaine have been obtained with TOF-SIMS of the single-cell organism Paramecium.