Proton mobility and main fragmentation pathways of protonated lysylglycine

Mechanistic Investigations on N-Cα Bond Cleavages in Dibasic Peptides Containing Internal Lys and Arg Residues

The model nonapeptide AAARAAKAG* (* indicates amide) is used to explore N-C^α bond fragmentation under CID-MS conditions. Neighboring group participation and the effect of positioning of Lys and Arg residues on N-C^α bond cleavage is established using a library of synthetic peptide analogues. The importance of the Arg residue at position 4 and the i to i+3 spacing between Arg and Lys residues in determining the formation of the N-C^α bond cleaved product ions (c_n) is demonstrated by a comparative MS study of positional variants in analogue peptides. The effect of shortening of the Lys side chain has been established using ornithine (Orn) and diaminobutyric acid (Dab) analogues. The involvement of the Lys residue in mediating the N-C^α bond cleavage is further probed using N^ε-dimethyl and isotopically labeled ¹⁵N^α, ε lysine residues. MSⁿ experiments reveal that the c₆ ion originates from a doubly charged dehydrated b₈ ion [b₈-18]²⁺. The mechanism of this unusual fragmentation process has been probed by using position 8 analogues (Gly, Ala, and Aib). A plausible mechanism is proposed for the origin of the c₆ ion, which involves C-terminus lactam formation followed by transannular cyclization and dehydration. The results presented in this study highlight the role of reactive side chain functionalities in promoting noncanonical fragmentation pathways.

A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation

Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. Graphical Abstract ᅟ.

Gas-phase fragmentation of protonated piplartine and its fungal metabolites using tandem mass spectrometry and computational chemistry

Piplartine, an alkaloid produced by plants in the genus Piper, displays promising anticancer activity. Understanding the gas-phase fragmentation of piplartine by electrospray ionization tandem mass spectrometry can be a useful tool to characterize biotransformed compounds produced by in vitro and in vivo metabolism studies. As part of our efforts to understand natural product fragmentation in electrospray ionization tandem mass spectrometry, the gas-phase fragmentation of piplartine and its two metabolites 3,4-dihydropiplartine and 8,9-dihydropiplartine, produced by the endophytic fungus Penicillium crustosum VR4 biotransformation, were systematically investigated. Proposed fragmentation reactions were supported by ESI-MS/MS data and computational thermochemistry. Cleavage of the C-7 and N-amide bond, followed by the formation of an acylium ion, were characteristic fragmentation reactions of piplartine and its analogs. The production of the acylium ion was followed by three consecutive and competitive reactions that involved methyl and methoxyl radical eliminations and neutral CO elimination, followed by the formation of a four-member ring with a stabilized tertiary carbocation. The absence of a double bond between carbons C-8 and C-9 in 8,9-dihydropiplartine destabilized the acylium ion and resulted in a fragmentation pathway not observed for piplartine and 3,4-dihydropiplartine. These results contribute to the further understanding of alkaloid gas-phase fragmentation and the future identification of piplartine metabolites and analogs using tandem mass spectrometry techniques. Copyright © 2017 John Wiley & Sons, Ltd.

Tandem mass spectrometric analysis of novel peptide-modified gemini surfactants used as gene delivery vectors

Diquaternary ammonium gemini surfactants have emerged as effective gene delivery vectors. A novel series of 11 peptide-modified compounds was synthesized, showing promising results in delivering genetic materials. The purpose of this work is to elucidate the tandem mass spectrometric (MS/MS) dissociation behavior of these novel molecules establishing a generalized MS/MS fingerprint. Exact mass measurements were achieved using a hybrid quadrupole orthogonal time-of-flight mass spectrometer, and a multi-stage MS/MS analysis was conducted using a triple quadrupole-linear ion trap mass spectrometer. Both instruments were operated in the positive ionization mode and are equipped with electrospray ionization. Abundant triply charged [M+H]³⁺ species were observed in the single-stage analysis of all the evaluated compounds with mass accuracies of less than 8 ppm in mass error. MS/MS analysis showed that the evaluated gemini surfactants exhibited peptide-related dissociation characteristics because of the presence of amino acids within the compounds' spacer region. In particular, diagnostic product ions were originated from the neutral loss of ammonia from the amino acids' side chain resulting in the formation of pipecolic acid at the N-terminus part of the gemini surfactants. In addition, a charge-directed amide bond cleavage was initiated by the amino acids' side chain producing a protonated α-amino-ε-caprolactam ion and its complimentary C-terminus ion that contains quaternary amines. MS/MS and MS³ analysis revealed common fragmentation behavior among all tested compounds, resulting in the production of a universal MS/MS fragmentation pathway. Copyright © 2017 John Wiley & Sons, Ltd.

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

The quantum chemical mass spectrometry for materials science (QCMS²) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS² framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. Graphical Abstract ᅟ.

Even-electron [M-H](+) ions generated by loss of AgH from argentinated peptides with N-terminal imine groups

RATIONALE

Experiments were performed to probe the creation of apparent even-electron, [M-H](+) ions by CID of Ag-cationized peptides with N-terminal imine groups (Schiff bases).

METHODS

Imine-modified peptides were prepared using condensation reactions with aldehydes. Ag(+) -cationized precursors were generated by electrospray ionization (ESI). Tandem mass spectrometry (MS(n) ) and collision-induced dissociation (CID) were performed using a linear ion trap mass spectrometer.

RESULTS

Loss of AgH from peptide [M + Ag](+) ions, at the MS/MS stage, creates closed-shell [M-H](+) ions from imine-modified peptides. Isotope labeling unambiguously identifies the imine C-H group as the source of H eliminated in AgH. Subsequent CID of the [M-H](+) ions generated sequence ions that are analogous to those produced from [M + H](+) ions of the imine-modified peptides.

CONCLUSIONS

Experiments show (a) formation of novel even-electron peptide cations by CID and (b) the extent to which sequence ions (conventional b, a and y ions) are generated from peptides with fixed charge site and thus lacking a conventional mobile proton.

The role of basic residues in the fragmentation process of the lysine rich cell-penetrating peptide TP10

Selective cleavage effect of basic residues in the fragmentation of short peptides has been studied intensively. In contrast, the role of basic residues in the degradation of large peptides, such as cell-penetrating peptides, is largely unknown. In this work, the fragmentation of a 21 residues cell-penetrating peptide TP10 containing four lysine residues was studied by collision-induced dissociation mass spectrometry and computation methods. The influence of lysine residues on amide bond cleavage and fragmentation products was investigated. The results revealed that the selective cleavage effect of lysine residue did not present when the adjacent lysine residues in TP10 were both protonated. The localized high positive charge density might be the reason of preventing the mobile proton from migrating to the amide bonds in this part of the peptide. In contrast, the mobile proton preferred to reside in the N-terminal part of TP10 which had less positive charge. This preference gave more information of the peptide sequence in the mass spectrometry study and was helpful for stabilizing the C-terminal part of TP10, in which the basic lysine residues were preserved and crucial to the cell-penetrating process.

Peptide dimethylation: fragmentation control via distancing the dimethylamino group

Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a1 ions. The advantageous generation of a1 ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ω-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ω-dimethylamino acids of systematically increasing alkyl chain lengths is reported.

Selective collision-induced fragmentation of ortho-hydroxybenzyl-aminated lysyl-containing tryptic peptides

RATIONALE

In protein studies that employ tandem mass spectrometry the manipulation of protonated peptide fragmentation through exclusive dissociation pathways may be preferred in some applications over the comprehensive amide backbone fragmentation that is typically observed. In this study, we characterized the selective cleavage of the side-chain Cζ-Nε bond of peptides with ortho-hydroxybenzyl-aminated lysine residues.

METHODS

Internal lysyl residues of representative peptides were derivatized via reductive amination with ortho-hydroxybenzaldehyde. The modified peptides were analyzed using collision-induced dissociation (CID) on an Orbitrap tandem mass spectrometer. Theoretical calculations using computational methods (density functional theory) were performed to investigate the potential dissociation mechanisms for the Cζ-Nε bond of the derivatized lysyl residue resulting in the formation of the observed product ions.

RESULTS

Tandem mass spectra of the derivatized peptide ions exhibit product peaks corresponding to selective cleavage of the side-chain Cζ-Nε bond that links the derivative to lysine. The ortho-hydroxybenzyl derivative is released either as a neutral moiety [C7H6O1] or as a carbocation [C7H7O1](+) through competing pathways (retro-Michael versus Carbocation Elimination (CCE), respectively). The calculated transition state activation barriers indicate that the retro-Michael pathway is kinetically favored over CCE and both are favored over amide cleavage.

CONCLUSIONS

The application of ortho-hydroxybenzyl amination is a promising peptide derivatization scheme for promoting selective dissociation pathways in the tandem mass spectrometry of protonated peptides. This can be implemented in the rational development of peptide reactive reagents for applications that may benefit from selective fragmentation paths (including crosslinking or MRM reagents).

Selective cleavage enhanced by acetylating the side chain of lysine

Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide. After acetylation of the lysine side-chain, b(n)+ ions were the most abundant primary fragment products and the Lys(Ac)-Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side-chain of lysine promoted the selective cleavage of Lys-Xxx amide bond and generated much more information of the peptide backbone sequence. The results re-evaluate the selective cleavage due to the lysine basic side-chain and provide information for studying the post-translational modification of proteins and other bio-molecules containing Lys residues.

Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

BACKGROUND

Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations.

METHODS

MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds.

RESULTS

We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation.

CONCLUSIONS

These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification.

Substituent effects on the gas-phase fragmentation reactions of protonated peptides containing benzylamine-derivatized lysyl residues

Motivated by the need for chemical strategies designed to tune peptide fragmentation to selective cleavage reactions, benzyl ring substituent influence on the relative formation of carbocation elimination (CCE) products from peptides with benzylamine-derivatized lysyl residues has been examined using collision-induced dissociation (CID) tandem mass spectrometry. Unsubstituted benzylamine-derivatized peptides yield a mixture of products derived from amide backbone cleavage and CCE. The latter involves side-chain cleavage of the derivatized lysyl residue to form a benzylic carbocation [C(7)H(7)](+) and an intact peptide product ion [(MH(n))(n+) - (C(7)H(7))(+)]((n-1)+). The CCE pathway is contingent upon protonation of the secondary ε-amino group (N(ε)) of the derivatized lysyl residue. Using the Hammett methodology to evaluate the electronic contributions of benzyl ring substituents on chemical reactivity, a direct correlation was observed between changes in the CCE product ion intensity ratios (relative to backbone fragmentation) and the Hammett substituent constants, σ, of the corresponding substituents. There was no correlation between the substituent-influenced gas-phase proton affinity of N(ε) and the relative ratios of CCE product ions. However, a strong correlation was observed between the π orbital interaction energies (ΔE(int)) of the eliminated benzylic carbocation and the logarithm of the relative ratios, indicating the predominant factor in the CCE pathway is the substituent effect on the level of hyperconjugation and resonance stability of the eliminated benzylic carbocation. This work effectively demonstrates the applicability of σ (and ΔE(int)) as substituent selection parameters for the design of benzyl-based peptide-reactive reagents which tune CCE product formation as desired for specific applications.

The charge ratio between O and N on amide bonds: a new approach to the mobile proton model

The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.

Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry

Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.

The relative charge ratio between C and N atoms in amide bond acts as a key factor to determine peptide fragment efficiency in different charge states

The influence of charge state on the peptide dissociation behavior in tandem mass spectrometry (MS/MS) is worthy of discussion. Comparative studies of singly- and doubly-protonated peptide molecules are performed to explore the effect and mechanism of charge state on peptide fragmentation. In view of the charge-directed cleavage of protonated peptides described in the mobile proton model, radiolytic oxidation was applied to change the charge distribution of peptides but retain the sequence. Experimental studies of collision energy-dependent fragmentation efficiencies coupled with quantum chemical calculations indicated that the cleavage of ARRA and its side-chain oxidation products with oxygen atoms added followed a trend that doubly-protonated peptides fragment more easily than singly-protonated forms, while the oxidation product with the guanidine group deleted showed the opposite trend. By analyzing the charge distribution around the amide bonds, we found that the relative charge ratios between C and N atoms (Q(C)/Q(N)) in the amide bonds provided a reasonable explanation for peptide fragmentation efficiencies. An increase of the Q(C)/Q(N) value of the amide bond means that a peptide fragments more easily, and vice versa. The results described in this paper provide an experimental and calculation strategy for predicting peptide fragmentation efficiency.

Gas-phase fragmentation characteristics of benzyl-aminated lysyl-containing tryptic peptides

The fragmentation characteristics of peptides derivatized at the side-chain epsilon-amino group of lysyl residues via reductive amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic cleavage of the C(zeta)-N(epsilon) bond that links the benzyl derivative to the side-chain lysyl residue. This results in the elimination of the derivative as a benzylic or tropylium carbocation and a (n - 1)(+)-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway increases with increasing charge of the precursor ion. For the benzyl-modified tryptic peptides analyzed in this study, peaks representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed reaction contingent upon protonation of the secondary epsilon-amino group of the benzyl-derivatized lysyl side chain. If the secondary epsilon-amine is protonated, the elimination of the carbocation is observed. If the precursor is not protonated at the secondary epsilon-amine, backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective control over the relative abundance of product ions generated from the two pathways.

Effect of the His residue on the cyclization of b ions

The MS(n) spectra of the [M + H](+) and b(5) peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b(4) ions derived from the first four peptides. The MS(2) spectra of the [M + H](+) ions show a substantial series of b(n) ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b ions when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b(4) and b(5) ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b(n) ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b(5) structures, the b(4) ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b(4) and b(5) the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.

To b or not to b: the ongoing saga of peptide b ions

Modern soft ionization techniques readily produce protonated or multiply protonated peptides. Collision-induced dissociation (CID) of these protonated species is often used as a method to obtain sequence information. In many cases fragmentation occurs at amide bonds. When the charge resides on the C-terminal fragment so-called y ions are produced which are known to be protonated amino acids or truncated peptides. When the charge resides on the N-terminal fragment so-called b ions are produced. Often the sequence of y and b ions are essential for peptide sequencing. The b ions have many possible structures, a knowledge of which is useful in this sequencing. The structures of b ions are reviewed in the following with particular emphasis on the variation of structure with the number of amino acid residues in the b ion and the effect of peptide side chain on b ion structure. The recent discovery of full cyclization of larger b ions results in challenges in peptide sequencing. This aspect is discussed in detail.

Gas-phase proton-transfer pathways in protonated histidylglycine

Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized.

A study of b1+H2O and b1-ions in the product ion spectra of dipeptides containing N-terminal basic amino acid residues

The product ion spectra of approximately 200 dipeptides were acquired under low-energy conditions using a triple quadrupole mass spectrometer. The spectra of dipeptides containing an N-terminal arginine (R), histidine (H), or lysine (K) were observed to yield a b(1) + H(2)O ion corresponding to the protonated basic amino acid. This was equivalent to the y(1)-ion in the corresponding C-terminal isomer. The formation of a b(1) + H(2)O ion was not a significant fragmentation channel in any dipeptides analyzed including those containing a C-terminal basic amino acid unless they also contained an N-terminal basic amino acid. Occurring simultaneously and under equal energy conditions an apparent b(1)-ion was formed, which has its corresponding C-terminal equivalent in the y(1)-H(2)O ion. Energy resolved mass spectrometry (ERMS), deuterium labeling, and accurate mass experiments as well as data reported were used to show the relationships between the b(1)+H(2)O and b(1)-ions in the dipeptides containing an N-terminal basic amino acid and the y(1) and y(1)-H(2)O ions in the corresponding C-terminal isomers.

Infrared Spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton

The gas-phase structures of the protonated pentapeptide Leu-enkephalin and its main collision-induced dissociation (CID) product ions, b4 and a4, are investigated by means of infrared multiple-photon dissociation (IR-MPD) spectroscopy and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows accurate structural probing of the site of protonation and the rearrangement reactions that have taken place in CID. It is shown that the singly protonated Leu-enkephalin precursor is protonated on the N-terminus. The b4 fragment ion forms two types of structures: linear isomers with a C-terminal oxazolone ring, as well as cyclic peptide structures. For the former structure, two sites of proton attachment are observed, on the N-terminus and on the oxazolone ring nitrogen, as shown in a previous communication (Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2005, 127, 17154-17155). Upon leaving the ions for longer radiative cooling delays in the ion cyclotron resonance (ICR) cell prior to IR spectroscopic investigation, one observes a gradual decrease in the relative population of oxazolone-protonated b4 and a corresponding increase in N-terminal-protonated b4. This experimentally demonstrates that the mobile proton is transferred between two sites in a gas-phase peptide ion and allows one to rationalize how the proton moves around the molecule in the dissociation process. The a4 fragment, which is predominantly formed via b4, is also confirmed to adopt two types of structures: linear imine-type structures, and cyclic structures; the former isomers are exclusively protonated on the N-terminus in sharp contrast to b4, where a mixture of protonation sites was found. The presence of cyclic b4 and a4 fragment ions is the first direct experimental proof that fully cyclic structures are formed in CID. These results suggest that their presence is significant, thus lending strong support to the recently discovered peptide fragmentation pathways (Harrison, A. G.; Young, A. B.; Bleiholder, B.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2006, 128, 10364-10365) that result in scrambling of the amino acid sequence upon CID.

Neutral loss of water from the b ions with histidine at the C-terminus and formation of the c ions involving lysine side chains

Neutral loss of water from the amide bond induced by the His side chain has been reported. The proposed fragmentation pathway is a retro-Ritter reaction catalyzed by the imidazole nitrogen. In our MS/MS study of the neuropeptide GAHKNYLRFamide, we observed that the neutral loss of water from the b(3) ion is abundant. The b(3) ion has a His residue at the C-terminus. As reported previously, in the b ions with His at the C-terminus, the imidazole residue is connected to the carbonyl carbon to form a five-membered ring. Therefore, it is unlikely that the neutral loss of water from the b(3) ion is catalyzed by the imidazole nitrogen. Through MS2 and MS3 studies of a synthetic peptide standard AGHKLL and its chemically labeled and isotope-encoded forms, we discovered that the water loss from the b(3) ion involves the carbonyl group of His, the hydrogen connected to the alpha-carbon of Gly, and the amide hydrogen of His. We also discovered the formation of an unusual c(x) ion in peptides with a Lys or Arg residue at the (x + 1) position of the peptide.

Investigation of intramolecular proton migration in a series of model, metal-cationized tripeptides using in situ generation of an isotope label

In this study we used an isotope label, generated in situ, to investigate intramolecular proton migration or scrambling during formation of [b(2)+17+Li](+) products by collision-induced dissociation (CID) of Li(+)-cationized tripeptides. To generate the isotope label, we used a McLafferty-type rearrangement of N-terminally acetylated, C-terminal peptide tert-butyl esters in which all amide positions were exchanged with deuterium. Using a set of small, model peptides, we show that intramolecular proton scrambling occurs during CID, particularly amongst adjacent sites along a peptide backbone, on the time scales employed for low-energy collisional activation in an ion-trap mass spectrometer.

Simple b ions have cyclic oxazolone structures. A neutralization-reionization mass spectrometric and computational study of oxazolone radicals

The 2-methyloxazol-5-on-2-yl radical (3) and its deuterium labeled analogs were generated in the gas-phase by femtosecond electron-transfer and studied by neutralization-reionization mass spectrometry and quantum chemical calculations. Radical 3 undergoes fast dissociation by ring opening and elimination of CO and CH(3)CO. Loss of hydrogen is less abundant and involves hydrogen atoms from both the ring and side-chain positions. The experimental results are corroborated by the analysis of the potential energy surface of the ground electronic state in 3 using density functional, perturbational, and coupled-cluster theories up to CCSD(T) and extrapolated to the 6-311 ++ G(3df,2p) basis set. RRKM calculations of radical dissociations gave branching ratios for loss of CO and H that were k(CO)/k(H) > 10 over an 80-300 kJ mol(-1) range of internal energies. The driving force for the dissociations of 3 is provided by large Franck-Condon effects on vertical neutralization and possibly from involvement of excited electronic states. Calculations also provided the adiabatic ionization energy of 3, IE(adiab) = 5.48 eV and vertical recombination energy of cation 3(+), RE(vert) = 4.70 eV. The present results strongly indicate that oxazolone structures can explain fragmentations of b-type peptide ions upon electron capture, contrary to previous speculations.

Fragmentation pathways of protonated peptides

The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the 'mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the 'pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented.

Intramolecular Migration of Amide Hydrogens in Protonated Peptides upon Collisional Activation

Presently different opinions exist as to the degree of scrambling of amide hydrogens in gaseous protonated peptides and proteins upon collisional activation in tandem mass spectrometry experiments. This unsettled controversy is not trivial, since only a very low degree of scrambling is tolerable if collision-induced dissociation (CID) should provide reliable site-specific information from (1)H/(2)H exchange experiments. We have explored a series of unique, regioselectively deuterium-labeled peptides as model systems to probe for intramolecular amide hydrogen migration under low-energy collisional activation in an orthogonal quadrupole time-of-flight electrospray ionization (Q-TOF ESI) mass spectrometer. These peptides contain a C-terminal receptor-binding sequence and an N-terminal nonbinding region. When the peptides form a receptor complex, the amide hydrogens of the interacting sequences are protected against exchange with the solvent, while the amide hydrogens of the nonbinding sequences exchange rapidly with the solvent. We have utilized such long-lived complexes to generate peptides labeled with deuterium in either the binding or nonbinding region, and the expected regioselectivity of this labeling was confirmed after pepsin proteolysis. CID of such deuterated peptides, [M + 2H](2+), yielded fragment ions (b- and y-ions) having a deuterium content that resemble the theoretical values calculated for 100% scrambling. Thus, complete randomization of all hydrogen atoms attached to nitrogen and oxygen occurs in the gaseous peptide ion prior to its dissociation.

Formation and reactions of clusters in the gas phase: small peptides and carboxylic acids

The cluster formation of seventeen small dipeptides with different primary structures and vanillic acid was investigated by means of a neutral laser desorption and supersonic beam expansion followed by multi photon ionization time of flight mass spectrometry. The structures of these clusters have been characterized by mass spectrometric methods as well as by DFT calculations. It is shown that the structure of the cluster from a dipeptide and vanillic acid is described by a hydrogen bond between the phenolic group of the vanillic acid and the N-terminal amino function of the dipeptide. The intensity of the cluster ion and the main fragmentation product, the protonated peptide ion, can be linked to the proton affinity of the peptide. Furthermore the fragmentation reactions of the protonated peptide are accompanied by extensive hydrogen rearrangements yielding both a and y fragments. The intensities of these fragments follow the proton affinity of the dipeptide.

Towards understanding the tandem mass spectra of protonated oligopeptides. 1: mechanism of amide bond cleavage

The mechanism of the cleavage of protonated amide bonds of oligopeptides is discussed in detail exploring the major energetic, kinetic, and entropy factors that determine the accessibility of the b(x)-y(z) (Paizs, B.; Suhai, S. Rapid Commun. Mass Spectrom. 2002, 16, 375) and "diketopiperazine" (Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. Anal. Chem. 1993, 65, 1594) pathways. General considerations indicate that under low-energy collision conditions the majority of the sequence ions of protonated oligopeptides are formed on the b(x)-y(z) pathways which are energetically, kinetically, and entropically accessible. This is due to the facts that (1).the corresponding reactive configurations (amide N protonated species) can easily be formed during ion excitation, (2). most of the protonated nitrogens are stabilized by nearby amide oxygens making the spatial arrangement of the two amide bonds (the protonated and its N-terminal neighbor) involved in oxazolone formation entropically favored. On the other hand, formation of y ions on the diketopiperazine pathways is either kinetically or energetically or entropically controlled. The energetic control is due to the significant ring strain of small cyclic peptides that are co-formed with y ions (truncated protonated peptides) similar in size to the original peptide. The entropy control precludes formation of y ions much smaller than the original peptide since the attacking N-terminal amino group can rarely get close to the protonated amide bond buried by amide oxygens. Modeling the b(x)-y(z) pathways of protonated pentaalanine leads for the first time to semi-quantitative understanding of the tandem mass spectra of a protonated oligopeptide. Both the amide nitrogen protonated structures (reactive configurations for the amide bond cleavage) and the corresponding b(x)-y(z) transition structures are energetically more favored if protonation occurs closer to the C-terminus, e.g., considering these points the Ala(4)-Ala(5) amide bond is more favored than Ala(3)-Ala(4), and Ala(3)-Ala(4) is more favored than Ala(2)-Ala(3). This fact explains the increasing ion abundances observed for the b(2)/y(3), b(3)/y(2), and b(4)/y(1) ion pairs in the metastable ion and low-energy collision induced mass spectra (Yalcin, T.; Csizmadia, I. G.; Peterson, M. B.; Harrison, A. G. J. Am. Soc. Mass Spectrom. 1996, 7, 233) of protonated pentaalanine. A linear free-energy relationship is used to approximate the ratio of the b(x) and y(z) ions on the particular b(x)-y(z) pathways. Applying the necessary proton affinities such considerations satisfactorily explain for example dominance of the b(4) ion over y(1) and the similar b(3) and y(2) ion intensities observed for the metastable ion and low-energy collision induced mass spectra.