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

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.