Fragmentation of deprotonated amino acids in atmospheric pressure chemical ionization

Protein amino acids (AAs) were ionized by atmospheric pressure chemical ionization (APCI) and fragmentation of the deprotonated molecules was investigated. Typical fragment anions were [M−H−NH3]−, [M−H−H2O]−, and [M−H−CO2]−. AAs which only generated the [M−H−NH3]− fragment ion were arginine, histidine, lysine, phenylalanine, and tyrosine, while threonine only produced the [M−H−CO2]− fragment ion. Asparagine and glutamine generated the [M−H−NH3]− and [M−H−H2O]− fragment ions, while glutamic acid generated the [M−H−H2O]− and [M−H−CO2]− fragment ions. Aspartic acid produced all the three fragment anions. AAs which did not generate the negative fragment ions were alanine, cysteine, glycine, isoleucine, leucine, lysine, methionine, proline, serine, and valine. Differences in the fragmentation patterns of underivatized AAs were explained by their structural characteristics. The specific fragment anions could be used for differentiating the underivatized AAs.

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► Fragmentation of deprotonated amino acids was investigated.
► Arg, His, Lys, Phe, and Tyr only generated [M−H−NH3]−, while Thr only produced [M−H−CO2]−.
► Asn and Gln produced [M−H−NH3]− and [M−H−H2O]−.
► Glu produced [M−H−H2O]− and [M−H−CO2]−.
► Asp generated both [M−H−NH3]−, [M−H−H2O]−, and [M−H−CO2]−.