Stability of fuels on storage is a topic of major concern. Oxidation prone compounds are known to react with air oxygen to form polar oxygenated products that ultimately can precipitate as a gum. Ketones are such reactive compounds, and here they are analyzed in several materials. They are recorded in a diesel as a function of the degree of hydrodesulfurization (HDS). A ketone selective reagent is used to derivatize only ketones, thus avoiding confusion with other one oxygen-atom containing compounds. The analysis was done using ultrahigh resolution Orbitrap mass spectrometry. The alkanones that were present in the original material are removed through HDS. Plenty of mainly aromatic ketones are formed when the fuel is stored in contact with air. A heating oil was stored under near-ambient conditions and analyzed after 12 and 18 months. Aromatic ketones arose throughout the storage, but their pattern did not change with time. A phenol selective derivatization reagent was used to show that many ketones containing a total of two oxygen atoms are in fact hydroxyphenyl alkyl ketones. A sediment contained ketones possessing a total of one to five oxygen atoms. The advantage of using selective derivatization reagents to differentiate between isomers based on their functional groups is demonstrated.