Diagnosing the protonation site of b2 peptide fragment ions using IRMPD in the X-H (X = O, N, and C) stretching region

Protonated α-N-Acetyl Galactose Glycopeptide Dissociation Chemistry

We recently provided mass spectrometric, H/D labeling, and computational evidence of pyranose to furanose N-acetylated ion isomerization reactions that occurred prior to glycosidic bond cleavage in both O- and N-linked glycosylated amino acid model systems (Guan et al. Phys. Chem. Chem. Phys., 2021, 23, 23256-23266). These reactions occurred irrespective of the glycosidic linkage stereochemistry (α or β) and the N-acetylated hexose structure (GlcNAc or GalNAc). In the present article, we test the generality of the preceding findings by examining threonyl α-GalNAc-glycosylated peptides. We utilize computational chemistry to compare the various dissociation and isomerization pathways accessible with collisional activation. We then interrogate the structure(s) of the resulting charged glycan and peptide fragments with infrared "action" spectroscopy. Isomerization of the original pyranose, the protonated glycopeptide [AT(GalNAc)A+H]⁺, is predicted to be facile compared to direct dissociation, as is the glycosidic bond cleavage of the newly formed furanose form, i.e., furanose oxazolinium ion structures are predicted to predominate. IR action spectra for the m/z 204, C₈H₁₄N₁O₅⁺, glycan fragment population support this prediction. The IR action spectra of the complementary m/z 262 peptide fragment were assigned as a mixture of the lowest-energy structures of [ATA+H]⁺ consistent with the literature. If general, the change to a furanose m/z 204 product ion structure fundamentally alters the ion population available for MS³ dissociation and glycopeptide sequence identification.

Two-Color IRMPD Applied to Conformationally Complex Ions: Probing Cold Ion Structure and Hot Ion Unfolding

Two-color infrared multiphoton dissociation (2C-IRMPD) spectroscopy is a technique that mitigates spectral distortions due to nonlinear absorption that is inherent to one-color IRMPD. We use a 2C-IRMPD scheme that incorporates two independently tunable IR sources, providing considerable control over the internal energy content and type of spectrum obtained by varying the trap temperature, the time delays and fluences of the two infrared lasers, and whether the first or second laser wavelength is scanned. In this work, we describe the application of this variant of 2C-IRMPD to conformationally complex peptide ions. The 2C-IRMPD technique is used to record near-linear action spectra of both cations and anions with temperatures ranging from 10 to 300 K. We also determine the conditions under which it is possible to record IR spectra of single conformers in a conformational mixture. Furthermore, we demonstrate the capability of the technique to explore conformational unfolding by recording IR spectra with widely varying internal energy in the ion. The protonated peptide ions YGGFL (NH₃⁺-Tyr-Gly-Gly-Phe-Leu, Leu-enkephalin) and YGPAA (NH₃⁺-Tyr-Gly-Pro-Ala-Ala) are used as model systems for exploring the advantages and disadvantages of the method when applied to conformationally complex ions.

Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides

Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes ([G_xR+2H]²⁺ and [A_xR+2H]²⁺, x = 2-5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b₂-y_N-2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.

Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase

The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.

Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide

The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b₂ ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b₂ ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b₂ ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b₂ ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group. Graphical Abstract ᅟ.

Combined Liquid Chromatography-Infrared Ion Spectroscopy for Identification of Regioisomeric Drug Metabolites

High-performance liquid chromatography was used in combination with infrared ion spectroscopy for the identification of positional isomers of hydroxy-atorvastatins, the primary metabolites of the drug atorvastatin. The results demonstrate the direct applicability of infrared ion spectroscopy in the field of drug metabolism and, more generally, its promising role in state-of-the-art analytical laboratories for the identification of small molecules buried in complex mixtures. In combination with chromatographic separation, infrared spectroscopy of mass-selected ions provides a promising new route for the identification of the molecular structures of unknown m/z peaks in a mass spectrum. We demonstrate that currently existing experimental protocols allow the measurement of an IR spectrum from less than 10 ng of sample obtained in a collected HPLC fraction.

Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH₃-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in - and confirmation of - the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides. Graphical Abstract ᅟ.

Infrared ion spectroscopy in a modified quadrupole ion trap mass spectrometer at the FELIX free electron laser laboratory

We report on modifications made to a Paul-type quadrupole ion trap mass spectrometer and discuss its application in infrared ion spectroscopy experiments. Main modifications involve optical access to the trapped ions and hardware and software coupling to a variety of infrared laser sources at the FELIX infrared free electron laser laboratory. In comparison to previously described infrared ion spectroscopy experiments at the FELIX laboratory, we find significant improvements in efficiency and sensitivity. Effects of the trapping conditions of the ions on the IR multiple photon dissociation spectra are explored. Enhanced photo-dissociation is found at lower pressures in the ion trap. Spectra obtained under reduced pressure conditions are found to more closely mimic those obtained in the high-vacuum conditions of an Fourier transform ion cyclotron resonance mass spectrometer. A gas-mixing system is described enabling the controlled addition of a secondary gas into helium buffer gas flowing into the trap and allows for ion/molecule reactions in the trap. The electron transfer dissociation (ETD) option of the mass spectrometer allows for IR structure characterization of ETD-generated peptide dissociation products.

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.

Elusive Sulfurous Acid: Gas-Phase Basicity and IR Signature of the Protonated Species

The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres.

Structure and further fragmentation of significant [a3 + Na - H]+ ions from sodium-cationized peptides

A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na - H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na - H](+) ion needs to overcome several relatively high energetic barriers to form [b2 + Na - H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na - H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na - H](+) from the [a3 + Na - H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides.

Nuclear magnetic resonance structure elucidation of peptide b2 ions

Tandem mass spectrometry (MS/MS) is powerful for chemical identification but it is still insufficient for explicit ion structure determination. A strategy is introduced to elucidate MS fragment ion structures using NMR spectroscopy for the first time. In our experiments, precursor ions are dissociated at atmospheric pressure and the resulting fragment ions are identified by mass spectrometry but collected outside the mass spectrometer, making the subsequent NMR measurements possible. This new strategy has been applied to determine the chemical structure of the characteristic b2  fragment ion, a subject of longstanding debate in MS-based proteomics.

Investigation of bn-44 peptide fragments using high resolution mass spectrometry and isotope labeling

An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway.

Photo-fragmentation spectroscopy of benzylium and 1-phenylethyl cations

The electronic spectra of cold benzylium (C6H5-CH2 (+)) and 1-phenylethyl (C6H5-CH-CH3 (+)) cations have been recorded via photofragment spectroscopy. Benzylium and 1-phenylethyl cations produced from electrosprayed benzylamine and phenylethylamine solutions, respectively, were stored in a cryogenically cooled quadrupole ion trap and photodissociated by an OPO laser, scanned in parts of the UV and visible regions (600-225 nm). The electronic states and active vibrational modes of the benzylium and 1-phenylethyl cations as well as those of their tropylium or methyl tropylium isomers have been calculated with ab initio methods for comparison with the spectra observed. Sharp vibrational progressions are observed in the visible region while the absorption features are much broader in the UV. The visible spectrum of the benzylium cation is similar to that obtained in an argon tagging experiment [V. Dryza, N. Chalyavi, J. A. Sanelli, and E. J. Bieske, J. Chem. Phys. 137, 204304 (2012)], with an additional splitting assigned to Fermi resonances. The visible spectrum of the 1-phenylethyl cation also shows vibrational progressions. For both cations, the second electronic transition is observed in the UV, around 33,000 cm(-1) (4.1 eV) and shows a broadened vibrational progression. In both cases the S2 optimized geometry is non-planar. The third electronic transition observed around 40,000 cm(-1) (5.0 eV) is even broader with no apparent vibrational structures, which is indicative of either a fast non-radiative process or a very large change in geometry between the excited and the ground states. The oscillator strengths calculated for tropylium and methyl tropylium are weak. Therefore, these isomeric structures are most likely not responsible for these absorption features. Finally, the fragmentation pattern changes in the second and third electronic states: C2H2 loss becomes predominant at higher excitation energies, for both cations.

Zundel-type H-bonding in biomolecular ions

Using quantum chemical calculations and infrared multiphoton dissociation (IRMPD) spectroscopy in the fingerprint and X-H stretching regions, we demonstrate here that the all-Ala (b6) fragment ion features a macrocyclic structure with C(2) symmetry. For this structure, the ionizing proton is equally shared by the Ala(1) and Ala(4) amide oxygens in a Zundel-type symmetric (X…H(+)…X) H-bond.

Cation-π interactions in protonated phenylalkylamines

Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.

Spectroscopic identification of cyclic imide b2-ions from peptides containing Gln and Asn residues

In mass-spectrometry based peptide sequencing, formation of b- and y-type fragments by cleavage of the amide C-N bond constitutes the main dissociation pathway of protonated peptides under low-energy collision induced dissociation (CID). The structure of the b2 fragment ion from peptides containing glutamine (Gln) and asparagine (Asn) residues is investigated here by infrared ion spectroscopy using the free electron laser FELIX. The spectra are compared with theoretical spectra calculated using density functional theory for different possible isomeric structures as well as to experimental spectra of synthesized model systems. The spectra unambiguously show that the b2-ions do not possess the common oxazolone structure, nor do they possess the alternative diketopiperazine structure. Instead, cyclic imide structures are formed through nucleophilic attack by the amide nitrogen atom of the Gln and Asn side chains. The alternative pathway involving nucleophilic attack from the side-chain amide oxygen atom leading to cyclic isoimide structures, which had been suggested by several authors, can clearly be excluded based on the present IR spectra. This mechanism is perhaps surprising as the amide oxygen atom is considered to be the better nucleophile; however, computations show that the products formed via attack by the amide nitrogen are considerably lower in energy. Hence, b2-ions with Asn or Gln in the second position form structures with a five-membered succinimide or a six-membered glutarimide ring, respectively. b2-Ions formed from peptides with Asn in the first position are spectroscopically shown to possess the classical oxazolone structure.

From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry

Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(-) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic.

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.

Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap

We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.

Rearrangement pathways of the a (4) ion of protonated YGGFL characterized by IR spectroscopy and modeling

The structure of the a (4) ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by 'action' infrared spectroscopy in the 1000-2000 cm(-1) ('fingerprint') range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a (4) ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N- terminus and an amide group -CO-NH(2) at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008, 112, 1286). Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer's work.