A large proportion of allergic skin reactions are considered to be the result of skin exposure to small organic chemicals that possess the intrinsic ability to covalently modify skin proteins, either directly or following activation. In the absence of information about specific skin protein targets, studies of chemical modifications are limited to the use of model proteins. We have previously demonstrated that selected well known skin sensitizers (2,4-dinitro-1-chlorobenzene and phenyl salicylate) have the ability to covalently modify residues selectively on the model protein, human serum albumin. In the present work, we focus on the differences in covalent binding observed for two additional model proteins, human cytokeratin 14 and human cofilin, both constituent proteins of skin. Using matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) and nano LC-MS and -MS/MS strategies, the amino acid residues targeted by 2,4-dinitro-1-chlorobenzene on the two model proteins have been identified. In contrast, a structurally related non-sensitiser (2,4-dichloro-1-nitrobenzene) and a non-sensitising irritant (benzalkonium chloride) did not covalently modify the model proteins. Detailed examination of the results for the sensitizers indicate that reactive chemicals target nucleophilic amino acids residing in specific microenvironments of the 3D protein structure that are conducive to reactivity. This observation has important implications for the development of hapten-peptide binding assays. It is envisaged that the data from such assays will be integrated with outputs from other in vitro assays in the future to give a prediction of the sensitisation potential of novel chemicals.