RATIONALEDirect analysis mass spectrometry (DAMS) techniques offer increased speed of analysis without the need for sample preparation or prior separation. A feature of these techniques is that all ionisable species will typically be analysed at the same time which makes the ability to distinguish between isobaric compounds increasingly important.METHODSInvestigations have been carried out to distinguish isomeric compounds by mass spectrometry only, without the use of any separation technique, in order to further understand the capabilities of DAMS techniques. The work focused on commercially available isomeric amino‐sulfonamides, i.e. sulfalene, sulfameter, sulfamethoxypyridazine, sulfamonomethoxine, sulfadoxine, sulfadimethoxine, sulfisomidine, sulfamethazine, sulfamerazine, sulfaperine, sulfadiazine and sulfapyrazine.RESULTSAll the isomeric compounds investigated could be distinguished from each other based on their tandem mass (MS/MS) spectrum or failing that, based on their MS3 spectrum. Common fragmentation patterns/pathways were observed for groups of the sulfonamides and a rationale for the fragmentations observed is proposed. For the sulfonamides which contain a methoxy group on the pyrimidinyl, pyridazynil, or pyrazinyl ring, the fragmentation‐directing feature is the positioning of the methoxy group in the ortho position of the ring with respect to the sulfonamide bond. The presence of an ortho substituent precludes the formation of the product ion resulting from the loss of aniline.CONCLUSIONSThis work has demonstrated the usefulness of MSn fragmentation data in identifying and distinguishing isobaric structural isomers without the need for separation by high‐performance liquid chromatography (HPLC), allowing the identification of compounds by DAMS techniques. This work has also highlighted patterns in the product ion data which has led to a postulation of how the protonation preference of a molecule can affect the product ions observed and how the presence of ortho substituents can affect this initial protonation preference. Copyright © 2012 John Wiley & Sons, Ltd.