This study demonstrates the use of MALDI-TOF/TOF CID fragmentation for the identification of expected and “unexpected” side products in a complex mixture of melt polymerized poly(butylene adipate) (PBA), which aged at room temperature, unexposed to direct sunlight and extreme temperature fluxuations. Expected products include PBA structures terminated with butanediol, adipic acid and buteneol (due to dehydration during synthesis); as well as cyclic architectures with no terminal groups. Additionally, side products were observed containing “unexpected” terminal groups such as glycol, propenyl, methanol, and aldehydes. Low energy fragmentation pathways and computational data are presented to verify the structural assignments of the identified structures, followed by discussion of their probable origin. 1,5-Hydrogen shift reactions were identified as the major low-energy fragmentation pathway.