Fourier transform mass spectrometry (FTMS) is widely used to characterise the chemical complexity of mixtures, such as natural organic matter (NOM), petroleum, and agri-food products (including Scotch Whisky). Although electrospray ionisation (ESI) is by far the most widely used ionisation source in these studies, other ionisation techniques are available and may offer complimentary information. In a recent study, we found matrix free laser desorption/ionisation (LDI) to be effective for the analysis of Suwannee River fulvic acid (SRFA), and to provide complementary chemical insights. In this study, LDI along with Atmospheric Pressure Photoionisation (APPI) and Atmospheric Pressure Chemical Ionisation (APCI) were compared to ESI for the analysis of Scotch Whisky. High mass accuracy (54 ppb, mean) allowed for assignment of 86% of peaks, with 3993 unique molecular formulas identified from four representative samples analysed. All four ionisation techniques, performed in negative mode, identified thousands of formulas. Many were unique to each ionisation source, whilst 699 formulas were common to all techniques. Ions were identified in both deprotonated and radical anion forms. Our study highlights the importance of a multi ionisation source approach; we recommend that analysis of complex mixtures, especially novel ones, should not be limited solely to ESI.