Structure of Electron-Capture Dissociation Fragments from Charge-Tagged Peptides Probed by Tunable Infrared Multiple Photon Dissociation

Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer

The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.

How Symmetry Influences the Dissociation of Protonated Cyclic Peptides

Protonated cyclic dipeptides undergo collision-induced dissociation, and this reaction mechanism strongly depends on the symmetry and the nature of the residues. We review the main dissociation mechanism for a series of cyclic dipeptides, obtained through chemical dynamics simulations. The systems range from the symmetrical cyclo-(glycyl-glycyl), with two possible symmetrical protonation sites located on the peptide ring, to cyclo-(tyrosyl-prolyl), where the symmetry of protonation sites on the peptide ring is broken by the dissimilar nature of the different residues. Finally, cyclo-(phenylalanyl-histidyl) shows a completely asymmetric situation, with the proton located on one of the dipeptide side chains, which explains the peculiar fragmentation mechanism induced by shuttling the proton, whose efficiency is strongly dependent on the relative chirality of the residues.

Generation, Characterization, and Dissociation of Radical Cations Derived from Prolyl-glycyl-glycine

Radical cations of an aliphatic tripeptide prolyl-glycyl-glycine (PGG^•+) and its sequence ions [a₃ + H]^•+ and [b₂ - H]^•+ have been generated by collision-induced dissociation of the [Cu(Phen)(PGG)]^•2+ complex, where Phen = 1,10-phenanthroline. Infrared multiple photon dissociation spectroscopy, ion-molecule reaction experiments, and theoretical calculations have been used to investigate the structures of these ions. The unpaired electron in these three radical cations is located at different α-carbons. The PGG^•+ radical cation has a captodative structure with the radical at the α-carbon of the proline residue and the proton on the oxygen of the first amide group. This structure is at the global minimum on the potential energy surface (PES). By contrast, the [a₃ + H]^•+ and [b₂ - H]^•+ ions are not the lowest-energy structures on their respective PESs, and their radicals are formally located at the C-terminal and second α-carbons, respectively. Density functional theory calculations on the structures of the ternary copper(II) complex ion suggest that the charge-solvated isomer of the metal complex is the precursor ion that dissociates to give the PGG^•+ radical cation. The isomer of the complex in which PGG is bound as a zwitterion dissociates to give the [a₃ + H]^•+ and [b₂ - H]^•+ ions.

w-Type ions formed by electron transfer dissociation of Cys-containing peptides investigated by infrared ion spectroscopy

In mass spectrometry-based peptide sequencing, electron transfer dissociation (ETD) and electron capture dissociation (ECD) have become well-established fragmentation methods complementary to collision-induced dissociation. The dominant fragmentation pathways during ETD and ECD primarily involve the formation of c- and z^• -type ions by cleavage of the peptide backbone at the N─C_α bond, although neutral losses from amino acid side chains have also been observed. Residue-specific neutral side chain losses provide useful information when conducting database searching and de novo sequencing. Here, we use a combination of infrared ion spectroscopy and quantum-chemical calculations to assign the structures of two ETD-generated w-type fragment ions. These ions are spontaneously formed from ETD-generated z^• -type fragments by neutral loss of 33 Da in peptides containing a cysteine residue. Analysis of the infrared ion spectra confirms that these z^• -ions expel a thiol radical (SH^• ) and that a vinyl C═C group is formed at the cleavage site. z^• -type fragments containing a Cys residue but not at the cleavage site do not spontaneously expel a thiol radical, but only upon additional collisional activation after ETD.

Spectroscopic Characterization of an Extensive Set of c-Type Peptide Fragment Ions Formed by Electron Transfer Dissociation Suggests Exclusive Formation of Amide Isomers

Electron attachment dissociation (electron capture dissociation (ECD) and electron transfer dissociation (ETD)) applied to gaseous multiply protonated peptides leads predominantly to backbone N-C_α bond cleavages and the formation of c- and z-type fragment ions. The mechanisms involved in the formation of these ions have been the subject of much discussion. Here, we determine the molecular structures of an extensive set of c-type ions produced by ETD using infrared ion spectroscopy. Nine c₃- and c₄-ions are investigated to establish their C-terminal structure as either enol-imine or amide isomers by comparison of the experimental infrared spectra with quantum-chemically predicted spectra for both structural variants. The spectra suggest that all c-ions investigated possess an amide structure; the absence of the NH bending mode at approximately 1000-1200 cm^-1 serves as an important diagnostic feature.

Replacing H+ by Na+ or K+ in phosphopeptide anions and cations prevents electron capture dissociation

By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z₄ + H]^+● fragment ion-radicals of the R-C^●H-CONH- type, initially formed by N-C_α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [^●DAAR + H]⁺ isomers and used to assign structures to the action spectra. The potential energy surface of [^●DAAR + H]⁺ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [^●XAAR + H]⁺ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C_α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]^●-ETD fragments containing Asp, Asn, Glu, and Gln residues. Graphical Abstract ᅟ.

Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed. Graphical Abstract ᅟ.

Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy

Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the ‘omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H]²⁺. Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species.

Mass spectrometry is a leading method used for sequencing peptides and proteins by fragmentation followed by analysis of the sequence fragments. Here, the authors use infrared spectroscopy to characterize the structures of peptide fragments formed during electron transfer dissociation.

Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate

Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.

Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction

Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase.

Combining gas phase electron capture and IRMPD action spectroscopy to probe the electronic structure of a metastable reduced organometallic complex containing a non-innocent ligand

Gas-phase reduction of a Zn(ii) complex followed by IR spectroscopy shows that the incoming electron is localized on the metal rather than on the ligand.

Structural Characterization of the UV-Induced Fragmentation Products in an Ion Trap by Infrared Multiple Photon Dissociation Spectroscopy

Protonated cinchona alkaloids and their dimers undergo photochemical reaction in the gas phase, leading to UV-specific photofragments, not observed by collision-induced dissociation. Simultaneous coupling of UV and IR lasers with a Paul ion trap has been achieved for obtaining the vibrational spectrum of the fragments arising from the photodissociation. The structure of the photoproduced radical has been fully characterized by comparing the experimental spectrum to that simulated by DFT calculations.

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.

Renaissance of cation-radicals in mass spectrometry

This brief overview addresses the topic that was presented in the Thomson Medal Award session at the 19th International Mass Spectrometry Conference in Kyoto, Japan. Mass spectrometry of cation-radicals has enjoyed a remarkable renaissance thanks to the development of new methods for electron attachment to multiply charged peptide ions. The charge-reduced ions that are odd-electron species exhibit interesting reactivity that is useful for peptide and protein sequencing. The paper briefly reviews the fundamental aspects of the formation, energetics, and backbone dissociations of peptide cation-radicals.

Structural investigations of aroylhydrazones derived from nicotinic acid hydrazide in solid state and in solution

Structural forms of aroylhydrazones derived from nicotinic acid hydrazide have been studied in the solid state by FT-IR spectroscopy and in solution by NMR, UV-Vis and ATR spectroscopy. The studied compounds were N'-benzylidene-3-pyridinecarbohydrazide (1), N'-(2,4-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (2), N'-(5-chloro-2-hydroxyphenylmethylidene)-3-pyridinecarbohydrazide (3), and N'-(3,5-dichloro-2-hydroxymethoxyphenylmethylidene)-3-pyridinecarbohydrazide (4). The compound 1 adopted the most stable ketoamine form (form I, -CO-NH-N=C-) in the solid state as well as in various organic solvents. In mixtures of organic solvents with water the UV-Vis and ATR spectra implied intermolecular hydrogen bonding of 1 with water molecules. The presence of both tautomeric forms I and II (form II, -COH=N-N=C-) was proposed for the solid substance and highly concentrated solutions of 2, whereas form I was detected as the predominant one in diluted solutions. For compounds 3 and 4 a coexistence of forms I and III (form III, -CO-NH-NH-C=C-CO-) was noticed in the solid state and in polar protic organic solvents. The conversion to form III was induced by increasing the water content in the solvent mixtures. This process was the most pronounced for compound 4. When exposed to daylight, an appearance of a new band was observed during time in the UV-Vis spectrum of 4 in organic solvent/water 1/1 mixtures, which implied that tautomeric interconversion was most likely followed by E/Z isomerisation.

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.

Two-dimensional ECD FT-ICR mass spectrometry of peptides and glycopeptides

2D FT-ICR MS allows the correlation between precursor and fragment ions by modulating ion cyclotron radii for fragmentation modes with radius-dependent efficiency in the ICR cell without the need for prior ion isolation. This technique has been successfully applied to ion-molecule reactions, Collision-induced dissociation and infrared multiphoton dissociation. In this study, we used electron capture dissociation for 2D FT-ICR MS for the first time, and we recorded two-dimensional mass spectra of peptides and a mixture of glycopeptides that showed fragments that are characteristic of ECD for each of the precursor ions in the sample. We compare the sequence coverage obtained with 2D ECD FT-ICR MS with the sequence coverage obtained with ECD MS/MS and compare the sensitivities of both techniques. We demonstrate how 2D ECD FT-ICR MS can be implemented to identify peptides and glycopeptides for proteomics analysis.

Relative stability of peptide sequence ions generated by tandem mass spectrometry

We report the use of unimolecular dissociation by infrared radiation for gaseous multiphoton energy transfer to determine relative activation energy (E(a,laser)) for dissociation of peptide sequence ions. The sequence ions of interest are mass-isolated; the entire ion cloud is then irradiated with a continuous wave CO(2) laser, and the first order rate constant, k(d), is determined for each of a series of laser powers. Provided these conditions are met, a plot of the natural logarithm of k(d) versus the natural logarithm of laser power yields a straight line, whose slope provides a measure of E(a,laser). This method reproduces the E(a) values from blackbody radiative dissociation (BIRD) for the comparatively large, singly and doubly protonated bradykinin ions (nominally y ( 9 ) and y ( 9 ) ( 2+ )). The comparatively small sequence ion systems produce E(a,laser) values that are systematic underestimates of theoretical barriers calculated with density functional theory (DFT). However, the relative E(a,laser) values are in qualitative agreement with the mobile proton model and available theory. Additionally, novel protonated cyclic-dipeptide (diketopiperazine) fragmentation reactions are analyzed with DFT. FT-ICR MS provides access to sequence ions generated by electron capture dissociation, infrared multiphoton dissociation, and collisional activation methods (i.e., b ( n ), y ( m ) , c ( n ), z ( m ) ( • ) ions).

Electron transfer dissociation (ETD) of peptides containing intrachain disulfide bonds

The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation (ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were observed, including: c (odd electron), z (even electron), c-33 Da, z+33 Da, c+32 Da, and z-32 Da types of ions. The presence of these ions indicated cleavages both at the disulfide bond and the N-Cα backbone from a single electron transfer event. Mechanistic studies supported a mechanism whereby the N-Cα bond was cleaved first, and radical-driven reactions caused cleavage at either an S-S bond or an S-C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence coverage, accounting for 75%-100% of possible backbone fragmentation.

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

Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b(2) ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800-3800 cm(-1) range acquired on a table-top laser system. Combining this tunable laser with a high power CO(2) laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm(-1), corresponding to the asymmetric N-H stretch of the (nonprotonated) N-terminal NH(2) group, is a distinct vibrational signature of the ring-protonated oxazolone structure.

Visible and ultraviolet spectroscopy of gas phase protein ions

Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry: reduction of scintillation noise using Cadzow data processing

In two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FTICR-MS), scintillation noise, caused mostly by fluctuations in the number of ions in the ICR cell, is the leading cause for errors in spectrum interpretation. In this study, we adapted an algorithm based on singular value decomposition and first introduced by Cadzow et al. (IEE Proceedings Pt. F 1987, 134, 69) to 2D FTICR-MS and we measured its performance in terms of noise reduction without losing signal information in the 2D mass spectrum.

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.

Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics

Pyridiniummethylcarbonyl moieties that were previously designed on the basis of electronic structure analysis are now utilized as fixed-charge tags with tunable electronic properties to be used for N-terminal peptide derivatization and sequencing by electron-transfer dissociation. Dipeptides AK and KA were derivatized at the peptide N-terminus with 4-dimethylaminopyridinium-N-acetyl (DMAP-ac) and pyridinium-N-acetyl (pyrid-ac) tags of increasing intrinsic recombination energies. Upon the capture of a free electron or electron transfer from fluoranthene anions, (DMAP-ac-AK+H)(2+), (DMAP-ac-KA+H)(2+), (pyrid-ac-AK+H)(2+) and (pyrid-ac-KA+H)(2+) ions, as well as underivatized (AK+2H)(2+), completely dissociated. The fixed-charge tags steered the dissociation upon electron transfer to form abundant backbone N-C(α) bond cleavages, whereas the underivatized peptide mainly underwent H-atom and side-chain losses. Precursor ion structures for the tagged peptides were analyzed by an exhaustive conformational search combined with B3LYP/6-31+G(d,p) geometry optimization and single-point energy calculations in order to select the global energy minima. Structures, relative energies, transition states, ion-molecule complexes, and dissociation products were identified for several charge-reduced species from the tagged peptides. The electronic properties of the charge tags and their interactions with the peptide moieties are discussed. Electrospray ionization and electron-transfer dissociation of larger peptides are illustrated with a DMAP-tagged pentapeptide.

Influence of charge state and amino acid composition on hydrogen transfer in electron capture dissociation of peptides

Although conventional N-Cα bond cleavage in electron capture dissociation (ECD) of multiply-charged peptides generates a complementary c' and z(·) fragment pair, the N-Cα cleavage followed by hydrogen transfer from c' to z(·) fragments produces other fragments, namely c(·) and z'. In this study, the influence of charge state and amino acid composition on hydrogen transfer in ECD is described using sets of peptides. Hydrogen transferred ionic species such as c(·) and z' were observed in ECD spectra of doubly-protonated peptides, while the triply-protonated form did not demonstrate hydrogen transfer. The extent of hydrogen transfer in ECD of doubly-protonated peptides was dependent on constituent amino acids. The ECD of doubly-protonated peptides possessing numerous basic sites showed extensive hydrogen transfer compared with ECD of less basic peptides. The extent of hydrogen transfer is discussed from the viewpoints of the structure of peptide ions, the possibility of internal hydrogen bonding and intermediate lifetime of complex [c' + z(·)].

Backbone and side-chain specific dissociations of z ions from non-tryptic peptides

Backbone z-type fragment ions formed by electron-transfer dissociation (ETD) of doubly protonated peptides AAHAL, AHDAL, and AHADL were subjected to collisional activation and their dissociation products were studied by ETD-CID-MS(3) and MS(4). Electron structure theory calculations were performed to elucidate ion structures and reaction mechanisms. All z ions showed competitive eliminations of C(3)H(7) and C(4)H(8) from the C-terminal Leu side chain. The energetics and kinetics of these dissociations were studied computationally for the z(4) ion from AAHAL, and optimized structures are reported for several intermediates and transition states. RRKM calculations on the combined B3LYP and PMP2/6-311++G(2d,p) potential energy surface provided unimolecular rate constants that closely reproduced the experimental branching ratios for C(3)H(7) and C(4)H(8) eliminations. Mechanisms were also studied for the loss of CO(2) from z ions generated by ETD of AHDAL and AHADL and for a specific radical-induced Asp-C(alpha)-CO backbone cleavage. CID of the z ions under study did not produce any fragment ions that would indicate cascade backbone dissociations triggered by the radical sites. In contrast, the majority of backbone dissociations occurred at bonds that were remote from the radical sites (spin-remote dissociations) and were triggered by proton migrations that were analogous to those considered for standard peptide ion fragmentations.

The structure of deprotonated tri-alanine and its a3- fragment anion by IR spectroscopy

We present the first infrared spectra of a mass-selected deprotonated peptide anion (AlaAlaAla) and its decarboxylated fragment anion formed by collision induced dissociation. Spectra are obtained by IRMPD spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Spectra have been recorded over the 800-1800 cm(-1) spectral range and compared with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. These experiments suggest a carboxylate anion for [M-H](-) and an amide deprotonated (amidate) structure for the a(3) fragment anion [M-H-CO(2)](-). The frequency for the amidate carbonyl stretch occurring around 1555 +/- 5 cm(-1) has been confirmed by additional spectroscopic studies of the conjugated base of N-methylacetamide, which serves as a simple model system for the deprotonated amide linkage in a peptide anion.

Effect of peptide fragment size on the propensity of cyclization in collision-induced dissociation: oligoglycine b(2)-b(8)

The chemistry of peptide fragmentation by collision-induced dissociation (CID) is currently being reviewed, as a result of observations that the amino acid sequence of peptide fragments can change upon activation. This rearrangement mechanism is thought to be due to a head-to-tail cyclization reaction, where the N-terminal and C-terminal part of the fragment are fused into a macrocycle (= cyclic peptide) structure, thus "losing" the memory of the original sequence. We present a comprehensive study for a series of b fragment ions, from b(2) to b(8), based on the simplest amino acid residue glycine, to investigate the effect of peptide chain length on the appearance of macrocycle fragment structures. The CID product ions are structurally characterized with a range of gas-phase techniques, including isotope labeling, infrared photodissociation spectroscopy, gas-phase hydrogen/deuterium exchange (using CH(3)OD), and computational structure approaches. The combined insights from these results yield compelling evidence that smaller b(n) fragments (n = 2, 3) exclusively adopt oxazolone-type structures, whereas a mixture of oxazolone and macrocycle b fragment structures are formed for midsized b(n) fragments, where n = 4-7. As each of these chemical structures exchanges at different rates, it is possible to approximate the relative abundances using kinetic fits to the H/D exchange data. Under the conditions used here, the "slow"-exchanging macrocycle structure represents approximately 30% of the b ion population for b(6)-b(7), while the "fast"-exchanging oxazolone structure represents the remainder (70%). Intriguingly, for b(8) only the macrocycle structure is identified, which is also consistent with the "slow" kinetic rate in the HDX results. In a control experiment, a protonated cyclic peptide with 6 amino acid residues, cyclo(Gln-Trp-Phe-Gly-Leu-Met), is confirmed not to adopt an oxazolone structure, even upon collisional activation. These results demonstrate that in some cases larger macrocycle structures are surprisingly stable. While more studies are required to establish the general propensity for cyclization in b fragments, the implications from this study are troubling in terms of faulty sequence identification.

Activated-electron photodetachment dissociation for the structural characterization of protein polyanions

Multiply deprotonated anions [M - nH](n-) of large peptide mellitin, ubiquitin, and beta-casein proteins were subjected to laser irradiation at 260 nm in a quadrupole ion trap. For all compounds, the predominant event consecutive to laser irradiation was the detachment of an electron. The subsequent isolation and collisional activation of the oxidized [M - nH]((n-1)-*) resulted in extensive fragmentation of the peptide backbone. For mellitin peptide, nearly a complete series of c(*), z, and a(*), x product ions were observed. Applied to proteins, this technique, coined as activated-electron photodetachment dissociation (activated-EPD), achieved much more extensive sequence coverage than regular collision activated dissociation (CAD) on the even-electron components. Furthermore, the activated-EPD spectrum of beta-casein displayed phosphorylated fragment ions which suggest that the method is able to preserve part of the labile bonds of post-translational modifications. Activated-EPD is, therefore, a promising complementary technique to other dissociation techniques governed by radicals, i.e., electron capture dissociation (ECD), electron transfer dissociation (ETD), and electron detachment dissociation (EDD), for the structural characterization of large peptides and small proteins.

Evidence of diketopiperazine and oxazolone structures for HA b2+ ion

Peptide fragmentation can lead to an oxazolone or diketopiperazine b(2)(+) ion structure. IRMPD spectroscopy combined with computational modeling and gas-phase H/D exchange was used to study the structure of the b(2)(+) ion from protonated HAAAA. The experimental spectrum of the b(2)(+) ion matches both the experimental spectrum for the protonated cyclic dipeptide HA (a commercial diketopiperazine) and the theoretical spectrum for a diketopiperazine protonated at the imidazole pi nitrogen. A characteristic band at 1875 cm(-1) and increased abundance of the peaks at 1619 and 1683 cm(-1) indicate a second population corresponding to an oxazolone species. H/D exchange also shows a mixture of two populations consistent with a mixture of b(2)(+) ion diketopiperazine and oxazolone structures.

On the charge partitioning between c and z fragments formed after electron-capture induced dissociation of charge-tagged Lys-Lys and Ala-Lys dipeptide dications

Here we report on the charge partition between c and z fragments formed after femtosecond collisional electron-transfer from Cs atoms to charge-tagged peptide dications. Peptides chosen for study were Ala-Lys (AK) and Lys-Lys (KK) where one or both of the lysine epsilon-amino groups were trimethylated to provide one or two fixed charges. For peptides with only one charge tag, the other charge was obtained by protonation of an amino group. In some experiments the ammonium group was tagged by 18-crown-6-ether (CE). Since recombination energies decrease in the order: MeNH3+ > NMe4+ > MeNH3+(CE) > NMe4+(CE), it is possible to change the probability for the transferred electron to end up at either the N-terminal or the C-terminal residue by CE attachment. We find, however, that the individual recombination energies have little influence on the relative ratio between the yield of c and z ions as long as there are no mobile protons that can be transferred between the two fragments. Our results can be accounted for by the Utah-Washington model where the electron is captured into an amide pi* orbital that weakens the N-C(alpha) bond and causes its breakage, followed by proton, electron, or hydrogen transfer between the c and z fragments that stay together as an ion-molecule complex for some time. The data are also in accordance with the notion that an amide group competes with the charged groups for the electron. Electron capture by charged groups results in loss of small neutrals such as hydrogen and ammonia.

Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.

Probing the mechanism of electron capture and electron transfer dissociation using tags with variable electron affinity

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via beta-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl, and 3,5-dinitrobenzyl structural moieties, having a range of EA from -1.15 to +1.65 eV, excluding the propanyl group. Typical ECD or ETD backbone fragmentations are completely inhibited in peptides with substituent tags having EA over 1.00 eV, which are referred to as electron predators in this work. Nearly identical rates of electron capture by the dications substituted by the benzyl (EA = -1.15 eV) and 3-nitrobenzyl (EA = 1.00 eV) moieties are observed, which indicates the similarity of electron capture cross sections for the two derivatized peptides. This observation leads to the inference that electron capture kinetics are governed by the long-range electron-dication interaction and are not affected by side chain derivatives with positive EA. Once an electron is captured to high-n Rydberg states, however, through-space or through-bond electron transfer to the EA-tuning tags or low-n Rydberg states via potential curve crossing occurs in competition with transfer to the amide pi* orbital. The energetics of these processes are evaluated using time-dependent density functional theory with a series of reduced model systems. The intramolecular electron transfer process is modulated by structure-dependent hydrogen bonds and is heavily affected by the presence and type of electron-withdrawing groups in the EA-tuning tag. The anion radicals formed by electron predators have high proton affinities (approximately 1400 kJ/mol for the 3-nitrobenzyl anion radical) in comparison to other basic sites in the model peptide dication, facilitating exothermic proton transfer from one of the two sites of protonation. This interrupts the normal sequence of events in ECD or ETD, leading to backbone fragmentation by forming a stable radical intermediate. The implications which these results have for previously proposed ECD and ETD mechanisms are discussed.