Analysis of the expressed protein complement of cells requires knowledge of the diversity of post-translational modifications that can occur and which can be transient or permanent. The modifications range from amino acid changes through to the addition of macromolecules: lipid, carbohydrate or protein. Many variants of the common amino acids can occur, which can affect the structure or function of the protein. The major class of modification, however, is represented by glycosylation, N-linked, O-linked, or glycosylphosphatidylinositol(GPI)-linked. Such modifications have roles in protein stability and folding, targeting and recognition. Glycosylated proteins can be found in all cellular compartments and, intracellularly, O-GlcNAc modification is commonplace. Lipid modification of proteins (acylation, prenylation, GPI-anchoring) is also common, resulting in membrane association, and can play an important role in cell signalling. Targeting and turnover of proteins can also be mediated via covalent protein addition, for example by members of the ubiquitin family. Limited proteolysis as a post-translational modification will be discussed, focusing on the family of membrane protein secretases, in particular in relation to the Alzheimer's amyloid precursor protein. Finally, acetylcholinesterase will be used as a model example to illustrate the diversity of modifications occurring on a single protein.