Collision-induced dissociation and post-source decay of model dodecapeptide ions containing lysine and glycine

A comparison of positive and negative ion collision-induced dissociation for model heptapeptides with one basic residue

The effects of the identity and position of basic residues on peptide dissociation were explored in the positive and negative modes. Low-energy collision-induced dissociation (CID) was performed on singly protonated and deprotonated heptapeptides of the type: XAAAAAA, AAAXAAA, AAAAAXA and AAAAAAX, where X is arginine (R), lysine (K) or histidine (H) residues and A is alanine. For [M + H](+), the CID spectra are dominated by cleavages adjacent to the basic residues and the majority of the product ions contain the basic residues. The order of a basic residue's influence on fragmentation of [M + H](+) is arginine > histidine approximately lysine, which is also the order of decreasing gas-phase basicity for these amino acids. These results are consistent with the side chains of basic residues being positive ion charge sites and with the more basic arginine residues having a higher retention (i.e. sequestering) of the positive charge. In contrast, for [M-H](-) the identity and position of basic residues has almost no effect on backbone fragmentation. This is consistent with basic residues not being negative mode charge sites. For these peptides, more complete series of backbone fragments, which are important in the sequencing of unknowns, can be found in the negative mode. Spectra at both polarities contain C-terminal y-ions, but y(n)''(+) has two more hydrogens than the corresponding y(n)(-). Another major difference is the production of the N-terminal backbone series b(n)(+) in the positive mode and c(n)(-) in the negative mode. Thus, comparison of positive and negative ion spectra with an emphasis on searching for pairs of ions that differ by 2 Da (y(n)''(+) vs y(n)(-)) and by 15 Da (b(n)(+) vs c(n)(-)) may be a useful method for determining whether a product ion is generated from the C-terminal or the N-terminal end of a peptide. In addition, a characteristic elimination of NH=C=NH from arginine residues is observed for deprotonated peptides.

Negative ion dissociation of peptides containing hydroxyl side chains

The dissociation of deprotonated peptides containing hydroxyl side chains was studied by electrospray ionization coupled with Fourier transform ion cyclotron resonance (ESI-FTICR) via sustained off-resonance irradiation collision induced dissociation (SORI-CID). Dissociation under post-source decay (PSD) conditions was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). This work included hexapeptides with one residue of serine, threonine, or tyrosine and five inert alanine residues. During SORI-CID and PSD, dissociation of [M-H](-) yielded c- and y-ions. Side-chain losses of formaldehyde (HCHO) from serine-containing peptides, acetaldehyde (CH(3)CHO) from threonine-containing peptides, and 4-methylene-2,5-cycohexadienone (C(7)H(6)O) from tyrosine-containing peptides were generally observed in the negative ion PSD and SORI-CID spectra. Side-chain loss occurs much less from tyrosine-containing peptides than from serine- and threonine-containing peptides. This is probably due to the bulky side chain of tyrosine, resulting in steric hindrance and poor geometry for dissociation reactions. Additionally, a selective cleavage leading to the elimination of the C-terminal residue from [M-H](-) was observed from the peptides with serine and threonine at the C-terminus. This cleavage does not occur in the dissociation of peptides with an amide group at the C-terminus or peptides with neutral or basic residues at the C-terminus. It also does not occur with tyrosine at the C-terminus. Both the C-terminal carboxylic acid group and the hydroxyl side chain of the C-terminal residue must play important roles in the mechanism of C-terminal residue loss. A mechanism involving both the C-terminal carboxylic acid group and a hydroxyl side chain of serine and threonine is proposed.

In-source decay characteristics of peptides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In-source decay (ISD) of peptides, coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, has been examined to determine the influence of the matrix, the susceptibility of amino-acid residues to ISD, and the effect of extraction delay times. Out of nine di- and tri-hydroxybenzoic acids and three cinnamic derivatives tested, the most suitable matrix for ISD was 2,5-dihydroxybenzoic acid. The amine bond at Xxx-Gly and Xxx-Val residues was less susceptible than other amino-acid residues to ISD; however, the more sensitive residue(s) were not as clear. Using a peptide that gave the y(n)- and (z(n) + 2)-series product ions, it was confirmed that amide-bond cleavage (formation of the y(n)-series ions) accompanied metastable peaks, whereas metastable peaks were never observed with amine-bond cleavage [formation of the (z(n) + 2)-series ions]. Furthermore, abundant c(n)-series ions, which originate from amine-bond cleavage on the peptide backbone, were observed whenever a minimum delay time of 38 ns or continuous extraction was used to obtain spectra. These data indicate that amine-bond cleavage in ISD takes place on the ionization time scale before the energy randomization is completed.

Negative ion postsource decay time-of-flight mass spectrometry of peptides containing acidic amino acid residues

Acidic peptides have been studied by negative ion postsource decay (PSD) matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The peptides contained from 5 to 16 residues and were chosen on the basis of their patterns of the acidic residues. Using typical MALDI sample preparation techniques employing an acidic matrix, gastrin I (1-14), and epidermal mitosis inhibiting pentapeptide yielded much larger deprotonated ion signals, [M - H]-, than protonated ions, [M + H]+. This may be due to their absence of basic residues, coupled with their arrays of acidic residues. The PSD fragmentation of the peptide negative ions showed that an array of acidic residues, as in gastrin I (1-14), yielded simple spectra containing mainly backbone cleavage ions from the C-terminus. Hirudin (54-65), which contains two sets of two consecutive Glu residues, and fibrinopeptide A and fibrinopeptide B, with isolated acidic residues, also showed backbone cleavages as common fragment ions. In addition, the two sets of isolated consecutive amino acid residues in Cys(Bzl)84-CD4 (81-92) and hirudin (54-56) yielded internal ions from the cleavages at the (O=C)-NH bond between the acidic residues. Also observed were ions with unique side chain losses, such as the loss of C6H4O from a tyrosine residue and SCH2C6H5 and CH2C6H5 from a benzylated cysteine residue. Compared to the positive mode, the negative-ion PSD yielded fewer fragments which usually involved only one type of backbone cleavage (e.g., [Yn - H2O]-). These simple spectra aided interpretation. Overall, the acidic peptides studied yielded negative ion PSD spectra that were useful for peptide sequencing.

Gas-phase reactivity and molecular modeling studies on triply protonated dodecapeptides that contain four basic residues

Gas-phase deprotonation and hydrogen/deuterium (H/D) exchange reactions for ions from three model dodecapeptides were studied by Fourier transform ion cyclotron resonance mass spectrometry. Molecular dynamics calculations were employed to provide information on conformations and Coulomb energies. The peptides, (KGG)4, (K2G4)2, and K4G8, each contain four high basicity lysine residues and eight low basicity glycine residues; however, in the present work only three lysine residues were protonated. Proton transfer reactions with a series of reference amines revealed apparent gas-phase acidities in a narrow range of 207.3-209.6 kcal/mol, with deprotonation efficiencies following the order [K4G8 + 3H]3+ > [(KGG)4 + 3H]3+ > [(K2G4)2 + 3H]3+. The three ions also react similarly with d4-methanol: each exchanged a maximum of 23-25 of their 25 labile hydrogens, with the first 15-17 exchanges occurring at rate constants of (1.6-2.6) x 10(-11) cm3 molecule-1 s-1. The experimental results agree with molecular modeling findings of similar conformations and Coulomb energies for the three peptide ions. The [M + 3H]3+ data are compared to data obtained previously in our laboratory for the "fully" protonated [M + 4H]4+ (Zhang, X.; Ewing, N. P.; Cassady, C. J. Int. J. Mass Spectrom. Ion Phys., in press). For (KGG)4 and (K2G4)2, there is a marked difference in H/D exchange reactivity between 3+ ions and 4+ ions. The 4+ ions, which have diffuse conformations, slowly exchange only 14 hydrogens, whereas their more compact 3+ counterparts exchange 23-25 hydrogens at a 5-times greater rate. In contrast, the 3+ and 4+ ions of K4G8 have similar compact conformations and exchange reactivity. The results indicate that a multiply hydrogen-bonded intermediate between the deuterating reagent and the peptide ion is necessary for facile H/D exchange. The slower, incomplete H/D exchange of [(KGG)4 + 4H]4+ and [(K2G4)2 + 4H]4+ is attributed to the inability of their protonated lysine n-butylamino groups (which extend away from the peptide backbone) to form this intermediate.