Plants are constantly challenged by various biotic and abiotic stresses in nature. Boron toxicity have become one of the important abiotic stress factor for plants. Boron toxicity responses of plants is reflected by alterations in protein expression level, activity, location and concentration. In this study, we identified the proteins which respond to the boron excess stress in Daucus carota root cells, and examined the effects of niacin (nicotinamide) on the protein profiles of boron excess. Protein profile changes in responce to boron and niacin were compared with the control using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) gel electrophoresis. Protein bands of interest were excised from gel and digested by trypsin. The trypsin-digested peptides were analyzed on nanoLC-ESI-MS/MS. Six different proteins involved in plant defense system were identified in total [CR16 (Major allergen Dau c1), glutathion peroxidase, glyoxylase I, isocitrate dehydrogenase (NADP(+)), adenosyl homocysteinase, EDPG precursor)]. Our results clearly demonstrated the presence of boron and niacin in growth medium stimulated expression and synthesis of proteins role in plant defence mechanism.