Neurological diseases including Parkinson’s, Alzheimer’s and motor neurone disease are hallmarked by neuronal death with protein aggregation playing a pathological role. Misincorporation of non-protein amino acids (NPAA) into proteins is thought to play a pivotal role in the onset and progression of such ‘proteinopathies’, characterised by protein misfolding and accumulation. For example, in case of multiple sclerosis, incorporation of the NPAA azetidine-2-carboxylic acid (AZE) into the proline-rich myelin basic protein in place of proline has been hypothesised to trigger autoimmunity. To investigate the level of misincorporation of AZE into proteins, we performed in whole sample in gel digestion coupled with label-free shotgun proteomics on the neuroblastoma cell line SHSY-5Y cultured in the presence or absence of 500µM azetidine. Moreover, the potential ability of proline co-supplementation to lower AZE incorporation and thus, to prevent the toxic protein misfolding effects, was also explored. Label-free quantitative analysis was performed in MaxQuant and LFQ-Analyst, whilst PEAKS was used to analyse AZE incorporation efficiencies, and all spectra of interest were further manually curated. These analyses resulted in the identification of 467 peptide sequences containing AZE incorporation across 270 unique protein IDs. Subsequent pathway analyses revealed ‘systemic lupus erythematosus’, ‘prion disease’ and ‘Parkinson’s disease’ as statistically enriched terms. Moreover, azetidine treatment results in a strong unfolded protein response, which is partially rescued by the co-admission of proline. Taken together, these in vitro results strongly suggest a potential role for azetidine incorporation in protein to result in misfolding and production of aberrant proteoforms. Further animal studies combined with immunological analysis are needed to support these data.