•Selective detection of PAPS with LC–MS within 10min.•ZIC-pHILIC provided separation from potentially interfering ADP/ATP.•The multi-separation mechanisms of HILIC requires fine-tuning.•Ultracentrifugal filtration of cell samples for simple preparation. 3′-Phosphoadenosine-5′-phosphosulfate (PAPS) is a key player in the sulfation of biomolecules, but methods for selective measurements are lacking. A liquid chromatography–mass spectrometry (LC–MS) approach for measuring PAPS was developed. A central feature of the method was employing hydrophilic interaction liquid chromatography (HILIC), which is highly suited for separating very polar/charged compounds, and is compatible with electrospray MS. Using simple instrumentation, the analysis time per sample was below 10min and the method was characterized by easy sample preparation. The method was used to monitor decreasing levels of PAPS as function of sodium chlorate treatment (an inhibitor of PAPS synthesis) in whole-cell lysates as well as Golgi-fractions. The method allowed PAPS to be chromatographically separated from ADP and ATP, which can interfere with measurements if a less resolving LC–MS method is used.