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Abstract The isotopomeric ions of non‐isotope‐enriched biomolecules generated by nanoelectrospray ionization were selectively fragmented by collision‐induced dissociation in a triple‐quadrupole mass spectrometer. Using this technique, the influence of heavy isotopes, such as 13C or 18O, on the isotopic pattern of fragment ions is significantly enhanced compared with the dissociation of an entire group of non‐mass selected molecular ions. Dissociation of the +1 Da isotopomeric ions results in fragment ion doublets, allowing the determination of the number of carbon atoms in the fragment when the empirical formula of the precursor molecular ion is known. Dissociation of the +2 Da isotopomeric ions results in fragment ion triplets. On the basis of the carbon atom number of a fragment, the ion abundances of these triplets allow the determination of a heteroelement such as oxygen, containing a stable isotope two mass units heavier than the value of its principle isotope. The technique was applied to the determination of the elemental composition of the two main fragment ions of protonated 1‐alkenyl‐2‐acyl‐phosphatidylethanolamine (plasmenyl‐phosphatidylethanolamine). The results show that they are formed by a rearrangement resulting in two complementary fragment ions carrying the 1‐alkenyl and 2‐acyl substituent, respectively. Information on the elemental composition of fragment ions can be obtained by isotope‐selective tandem electrospray mass spectrometry using sample amounts in the low picomole range. © 1998 John Wiley & Sons, Ltd.
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