Decomposition products formed/released during ammonia fiber expansion (AFEX) and dilute acid (DA) pretreatment of corn stover (CS) were quantified using robust mass spectrometry based analytical platforms. Ammonolytic cleavage of cell wall ester linkages during AFEX resulted in the formation of acetamide (25 mg/g AFEX CS) and various phenolic amides (15 mg/g AFEX CS) that are effective nutrients for downstream fermentation. After ammonolysis, Maillard reactions with carbonyl-containing intermediates represent the second largest sink for ammonia during AFEX. On the other hand, several carboxylic acids were formed (e.g. 35 mg acetic acid/g DA CS) during DA pretreatment. Formation of furans was 36-fold lower for AFEX compared to DA treatment; while carboxylic acids (e.g. lactic and succinic acids) yield was 100-1000-fold lower during AFEX compared to previous reports using sodium hydroxide as pretreatment reagent. (C) 2010 Elsevier Ltd. All rights reserved.