Dissociation of protonated peptides: Structure elucidation, energetics and mechanisms by tandem mass spectrometry

In an effort to understanding peptide dissociation behavior in mass spectrometry, a thorough comparison study of surface-induced dissociation (SID) and collision-induced dissociation (CID) in the structural analysis of protonated peptides in the range of 300–1800 Da was conducted using tandem quadrupole and Fourier transform mass spectrometers (FTMS). Initially, on-resonance CID and sustained off-resonance irradiation (SORI)-CID processes were characterized by a “thermometer” molecule Cr(CO)₆ in an FTMS. The average internal energy deposition and internal energy distributions were obtained by fitting the experimental data to the known threshold photonion photonelectron coincidence (TPIPECO) data using a computer algorithm. A comparison study of SID, SORI-CID and on-resonance CID shows that SID provides much higher average internal energies and narrower energy distributions than the other two methods.; A study of singly protonated pentapeptides showed that selective cleavages at the last residue of the C-terminus were observed in peptides containing no basic residues. It was proposed that acidic hydrogen at the C-terminal carboxylic acid could induce this preferential cleavage. The origins of a* and b* ions were determined by resonant ejection experiments. It was mainly from the fragmentation of [MH-NH₃] + with a small fraction from the corresponding a and b ions.; The investigation of a set of angiotensin analogs show that charge state has dramatic effect on peptide dissociation. Non-selective cleavages were observed in singly protonated peptides while selective cleavages were obtained in doubly protonated peptides. Dominant cleavage at Pro in RVYIHPF indicates that alkylated amide nitrogens in the Pro enhance the formation of b/y singly protonated complementary ions.; An investigation of peptides containing two Asp or Glu residues and zero, one or two Arg shows the existence of acid-base interactions in the gas phase. The data illustrate that selective cleavages C-terminal to Asp were observed in both SORI-CID/FTMS and SID/quadrupole spectra. The preferential cleavage C-terminal to Glu observed in SORI-CID but not in SID suggests that the formation of 8-membered ring in Glu is rather slow and can only be observed in the long observation time window.