The EI‐MS fragmentation mechanisms of one bacterial sesquiterpene alcohol and four diterpene hydrocarbons were investigated using all 15 or 20 enzymatically synthesised (13C1)‐labelled isotopomers for each molecule. A position‐specific mass shift analysis (PMA) indicated the parts of the carbon backbone for each fragment ion that is relevant for its formation. Plausible fragmentation mechanisms were developed and further strengthened by HR‐MS/MS analyses.