Mass Spectrometry (Mass-Spec)

Mass spectrometry (MS) is a key tool in organic chemistry for determining the masses of molecules and their fragments. In simple terms: you ionize a molecule, create charged species, and then detect those based on their mass-to-charge (m/z) ratio. The full molecular ion sometimes appears, but often you’ll see the molecule break apart into smaller charged fragments (because radical fragments go undetected). For example, when a molecule loses an electron and becomes a radical cation, it can fragment further, and the MS only “sees” the positively charged pieces. 

In the set of tutorials, we’ll start with the fundamentals of MS: how the instrument works, how to read spectra (molecular ion, base peak, isotopic patterns, etc.). Then we’ll focus on a specific fragmentation mechanism known as the McLafferty rearrangement, this is especially important for carbonyl-containing molecules (ketones, esters) that have the α-β-γ sequence and a γ-hydrogen.  Finally, you’ll put everything into practice by working through problems where you predict fragment peaks, identify molecular ions, and recognise when the McLafferty rearrangement might be happening.