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Distinguishing N- and C-terminus ions for mass spectrometry sequencing of proteins without prior degradation.

Identifying complementary pairs of fragment ions, b-type vs y-type, is a key step in mass spectral sequencing of proteins without degradation prior to ionization. Observations that b-type ions tend to be less stable than y-type have been extended to carbonic anhydrase (29 kDa) as a model protein. Infrared multiphoton dissociation (IRMPD) of 24+, 27+, 30+ molecular ions shows y-type ions from complementary pairs require, on average, 27% longer irradiation times for onset of abundance decrease, while in nozzle/skimmer dissociation of all charge states, y-type ions require a 20% higher potential difference. In some cases, b-ion dissociation appears to accompany its formation, as its rate of increase with increasing energy deposition is far less than that of its y-complement.