The tremendous structural and isomeric diversity of lipids enables a wide range of their functions in nature but makes the identification of these biomolecules challenging. We distinguish and quantify isomeric lipids using cold ion UV fragmentation spectroscopy of their noncovalent complexes with aromatic amino acids and dipeptides. On the basis of structural simulations, specific isomer-sensitive aromatic "sensors" have been preselected for lipids of each studied class. Tyrosine appeared to be a good "sensor" to distinguish steroids and prostaglandins, which are rich in functional groups, while diphenylalanine is a better choice for sensing largely hydrophobic phospholipids. With this sensor, the relative concentrations of two isomeric glycerophospholipids mixed in solution have been determined with 3.3% accuracy, which should degrade only to 3.7% for a 14 s express measurement.