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Isotopic assignment in large-molecule mass spectra by fragmentation of a selected isotopic peak.

For large ( > 5 kDa) ionic species, Fourier transform ion cyclotron resonance instruments yield by far the highest mass accuracy. However, this can be compromised by misassignment of the isotopic content based on predicted natural abundances of the isotopic peaks. As an alternative method independent of natural abundance variations, high-resolution isolation and dissociation of a single isotopic peak yields a distribution of isotopic peak abundances characteristic of the isotopic content of the precursor peak. Accuracy is enhanced if the precursor peak is abundant and of minimum heavy isotope content, and if the product species is abundant and of intermediate mass. In addition, such spectra of the highest mass products are useful for identifying complementary product pairs, a key step in sequencing proteins and nucleotides.