Oat straw was treated with different chemical reagents to remove specific components from the cell walls. The effects of these treatments were investigated using traditional wet-chemical analyses and pyrolysis mass spectrometry (Py-MS) in both electron impact and chemical ionization modes. Separate treatments with permanganate and chlorite dissolved the major portion of the lignin, while alkaline peroxide treatment dissolved a proportion of the non-cellulose polysaccharides (NCPs). Combined chlorite and sodium hydroxide treatments removed most of the lignin and NCPs whereas peracetic acid treatment showed a slight decrease in both NCPs and lignin contents. Py-MS thus confirmed the wet chemistry results by showing reductions in the ion markers for both lignin and NCPs, where appropriate. In addition, Py-MS showed other changes, such as the removal of phenolic acids, in a single analysis while differences between the residues from permanganate and chlorite treatment were also observed even though the chemical analyses gave virtually identical results.