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.