Brevetoxins are a group of natural neurotoxins found in blooms of red tide algae. Previous electrospray mass spectrometry (ES-MS) studies show that all brevetoxins have high affinities for sodium ions, and they form abundant sodium adduct ions, [M + Na]+, in ES-MS, even when trace contamination is the only source of sodium ions. Attempts to obtain informative product ions from the collision-induced decomposition (CID) of [M + Na]+ brevetoxin precursor ions resulted only in uninformative sodium ion signals, even under elevated collision energies. In this study, a nano-ES-MS approach was developed wherein ammonium fluoride was used to form cationic [M + NH4]+ adducts of brevetoxin-2 and brevetoxin-3; a significant increase in the abundance of protonated brevetoxin molecules [M + H]+ also resulted, whereas the abundance of sodium adducts of brevetoxins [M + Na]+ was observed to decrease. Under CID, both [M + NH4]+ and [M + H]+ gave similar, abundant product ions and thus underwent the same types of fragmentation. This indicated that ammonium ions initially attached to brevetoxins forming [M + NH4]+ easily lose neutral ammonia in a first step in the gas phase, leaving protonated brevetoxin [M + H]+ to readily undergo further fragmentation under CID. Copyright © 2006 John Wiley & Sons, Ltd.