The spirolides are a family of marine biotoxins derived from the dinoflagellate Alexandrium ostenfeldii, recently isolated from contaminated shellfish and characterized. A crude phytoplankton extract has been extensively studied for mass spectrometric determination and characterization of several known spirolides and previously unreported compounds. The complex sample was initially analyzed by full-scan mass spectrometry in an ion-trap instrument, enabling identification of several components. Subsequent analysis by selected-ion monitoring in a triple-quadrupole instrument resulted in the confirmation of the identities of the compounds detected in the ion trap. Purification of the crude extract was performed using an automated mass-based fractionation system, yielding several fractions with different relative contributions of the spirolide components. Collision-induced dissociation (CID) in the triple-quadrupole instrument produced significant fragment ions for all identified species. Selective enrichment of some minor compounds in certain fractions enabled excellent CID spectra to be generated; this had previously been impossible, because of interferences from the major toxins present. Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry was then performed for accurate determination of the masses of MH+ ions of all the species present in the sample. Additionally, infrared multiphoton dissociation in the FTICR instrument generated elemental formulae for product ions, including those formed in the previous collisional activation experiments. Collection of these results and the fragmentation scheme proposed for the main component of the extract, 13-desmethyl spirolide C, from part I of this study, enabled elucidation of the structures of some uncharacterized spirolides and some biogenetically related compounds present at previously unreported masses.