The most prevalent of the ambient mass spectrometries, desorption electrospray ionisation (DESI), which provides highly sensitive mass spectrometry from surfaces without the constraint of vacuum, is compared with secondary ion mass spectrometry (SIMS). The potential of DESI has been demonstrated in a wide range of application areas, including forensics, homeland security, counterfeit detection of pharmaceuticals and biological analysis. As with all techniques, there are some disadvantages: DESI cannot generally desorb molecules that are strongly bound to surfaces; there are low signals from molecules with low ionisation efficiency; and the spatial resolution is currently limited to approximately 100 µm. For these studies, SIMS is more powerful, but the two mass spectrometries are highly complementary. DESI uses a gentler desorption mechanism to remove material from the surface than the sputtering involved in SIMS. In particular, large fragile molecules can be detected intact, rather than heavily fragmented as in SIMS. Here, we illustrate the complementarities of SIMS and DESI for the analysis of 18 industrially relevant organic molecules.