A comparison of negative and positive ion time-of-flight post-source decay mass spectrometry for peptides containing basic residues

Abstract

Nine peptides containing highly basic residues were studied by post-source decay (PSD) in a reflectron time-of-flight (TOF) mass spectrometer. Although these compounds produced more abundant yields of protonated ions, [M+H] +, by matrix-assisted laser desorption ionization (MALDI), deprotonated ions, [MH] −, were formed in sufficient intensities for study by tandem mass spectrometry (MS/MS). PSD was conducted in both the positive and negative ion modes. Peptide backbone cleavage involving the y-ion series is generally seen in both modes and the two Dalton difference in mass between y n ″ + and y n − can be useful in identifying these ions. For negative ions, PSD also generated c n − and (to a lesser extent) a n −, while b n + are produced from positive ions. When a peptide contains a mixture of acidic and basic residues, the negative PSD spectra are more complex and the locations of acidic residues dictate some fragmentations. The most extensive and abundant production of c n − occurs in peptides with no acidic residues. This suggests that the mechanism for c-ion formation does not involve a deprotonated side chain, but may invoke a mobile deprotonation site along the peptide amide backbone or may possibly involve a charge remote cleavage. Negative ion PSD of basic peptides yields structurally informative spectra that complement the positive data. Even highly basic peptides, such as ACTH (11–24), can be studied in the negative ion mode.