Electron capture in charge-tagged peptides. Evidence for the role of excited electronic states

Mechanistic Study into Free Radical-Activated Glycan Dissociations through Isotope-Labeled Cellobioses

Inspired by the electron-activated dissociation technique, the most potent tool for glycan characterization, we recently developed free radical reagents for glycan structural elucidation. However, the underlying mechanisms of free radical-induced glycan dissociation remain unclear and, therefore, hinder the rational optimization of the free radical reagents and the interpretation of tandem mass spectra, especially the accurate assignment of the relatively low-abundant but information-rich ions. In this work, we selectively incorporate the ¹³C and/or ¹⁸O isotopes into cellobiose to study the mechanisms for free radical-induced dissociation of glycans. The eight isotope-labeled cellobioses include 1-¹³C, 3-¹³C, 1'-¹³C, 2'-¹³C, 3'-¹³C, 4'-¹³C, 5'-¹³C, and 1'-¹³C-4-¹⁸O-cellobioses. Upon one-step collisional activation, cross-ring (X ions), glycosidic bond (Y-, Z-, and B-related ions), and combinational (Y₁ + ^0,4X₀ ion) cleavages are generated. These fragment ions can be unambiguously assigned and confirmed by the mass difference of isotope labeling. Importantly, the relatively low-abundant but information-rich ions, such as ^1,5X₀ + H, ^1,4X₀ + H, ^2,4X₀ + H-OH, Y₁ + ^0,4X₀, ^2,5X₁-H, ^3,5X₀-H, ^0,3X₀-H, ^1,4X₀-H, and B₂-3H, are confidently assigned. The mechanisms for the formations of these ions are investigated and supported by quantum chemical calculations. These ions are generally initiated by hydrogen abstraction followed by sequential β-elimination and/or radical migration. Here, the mechanistic study for free radical-induced glycan dissociation allows us to interpret all of the free radical-induced fragment ions accurately and, therefore, enables the differentiation of stereochemical isomers. Moreover, it provides fundamental knowledge for the subsequent development of bioinformatics tools to interpret the complex free radical-induced glycan spectra.

Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation

Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP⁺ and TMPP-Ac-NH₂/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.

Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure

In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.

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.

Dissociation of trivalent metal ion (Al(3+), Ga(3+), In(3+) and Rh(3+))--peptide complexes under electron capture dissociation conditions

RATIONALE

The electron capture dissociation (ECD) of proteins/peptides is affected by the nature of charge carrier. It has been reported that transition metal ions could tune the ECD pathway of peptides. To further explore the charge carrier effect of metal ions, ECD of peptides adducted with trivalent transition metal ions, including group IIIB (Al(3+), Ga(3+), and In(3+) ) and Rh(3+), were investigated and compared with that of the lanthanide ion (Ln(3+)).

METHODS

Bradykinin-derived peptides were used as model peptides to probe the dissociation pathways. The ECD experiments were performed on a Bruker APEX III 4.7T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.

RESULTS

Typical c-/z-ions with and without metal ions were observed in the ECD of peptides adducted with Group IIIB metal ions as charge carriers. Connection of non-metalated c-ions and metalated z-ions at the position of the serine residue indicated that serine is one of the binding sites of the metal ion on the model peptides. Typical slow heating ions, including metalated a-/b-ions and non-metalated y-ions, were generated in ECD of Rh(3+) -adducted peptides.

CONCLUSIONS

Based on the experimental results, it is proposed that (i) for Group IIIB metal ion-peptide complexes, the incoming electron is captured by the proton in the salt-bridge structures of precursor ions; (ii) for Rh(3+) -peptide complexes, the incoming electron is captured by the metal ion due to the formation of charge-solvated precursor ions formed through arginine residue-metal coordination. Our results indicate that the heterogeneity of precursor ions plays an important role for the ECD of metalated peptides.

Investigation of the Mechanism of Electron Capture and Electron Transfer Dissociation of Peptides with a Covalently Attached Free Radical Hydrogen Atom Scavenger

The mechanisms of electron capture and electron transfer dissociation (ECD and ETD) are investigated by covalently attaching a free-radical hydrogen atom scavenger to a peptide. The 2,2,6,6-tetramethylpiperidin-l-oxyl (TEMPO) radical was chosen as the scavenger due to its high hydrogen atom affinity (ca. 280 kJ/mol) and low electron affinity (ca. 0.45 ev), and was derivatized to the model peptide, FQX^TEMPOEEQQQTEDELQDK. The X^TEMPO residue represents a cysteinyl residue derivatized with an acetamido-TEMPO group. The acetamide group without TEMPO was also examined as a control. The gas phase proton affinity (882 kJ/mol) of TEMPO is similar to backbone amide carbonyls (889 kJ/mol), minimizing perturbation to internal solvation and sites of protonation of the derivatized peptides. Collision induced dissociation (CID) of the TEMPO tagged peptide dication generated stable odd-electron b and y type ions without indication of any TEMPO radical induced fragmentation initiated by hydrogen abstraction. The type and abundance of fragment ions observed in the CID spectra of the TEMPO and acetamide tagged peptides are very similar. However, ECD of the TEMPO labeled peptide dication yielded no backbone cleavage. We propose that a labile hydrogen atom in the charge reduced radical ions is scavenged by the TEMPO radical moiety, resulting in inhibition of N-C_α backbone cleavage processes. Supplemental activation after electron attachment (ETcaD) and CID of the charge-reduced precursor ion generated by electron transfer of the TEMPO tagged peptide dication produced a series of b + H (b^H) and y + H (y^H) ions along with some c ions having suppressed intensities, consistent with stable O-H bond formation at the TEMPO group. In summary, the results indicate that ECD and ETD backbone cleavage processes are inhibited by scavenging of a labile hydrogen atom by the localized TEMPO radical moiety. This observation supports the conjecture that ECD and ETD processes involve long-lived intermediates formed by electron capture/transfer in which a labile hydrogen atom is present and plays a key role with low energy processes leading to c and z ion formation. Ab initio and density functional calculations are performed to support our conclusion, which depends most importantly on the proton affinity, electron affinity and hydrogen atom affinity of the TEMPO moiety.

Suppression of peptide ion dissociation under electron capture: role of backbone amide hydrogen

RATIONALE

The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides.

METHODS

Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer.

RESULTS

Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared.

CONCLUSIONS

Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation.

Electron transfer reduction of the diazirine ring in gas-phase peptide ions. On the peculiar loss of [NH4O] from photoleucine

Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)(+[Symbol: see text]) cation-radicals undergo elimination of [NH(4)O] radicals and N(2)H(2) molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR +2H)(+[Symbol: see text]) cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized by multistage tandem mass spectrometry (MS(n)) and ion mobility measurements. The elimination of [NH(4)O] was elucidated with the help of (2)H, (15) N, and (18)O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)(+[Symbol: see text]) cation-radicals was found to reduce the diazirine ring. In contrast, backbone N - Cα bond dissociations that represent a 60%-75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states.

Mechanistic study on electron capture dissociation of the oligosaccharide-Mg²⁺ complex

Electron capture dissociation (ECD) has shown great potential in structural characterization of glycans. However, our current understanding of the glycan ECD process is inadequate for accurate interpretation of the complex glycan ECD spectra. Here, we present the first comprehensive theoretical investigation on the ECD fragmentation behavior of metal-adducted glycans, using the cellobiose-Mg²⁺ complex as the model system. Molecular dynamics simulation was carried out to determine the typical glycan-Mg²⁺ binding patterns and the lowest-energy conformer identified was used as the initial geometry for density functional theory-based theoretical modeling. It was found that the electron is preferentially captured by Mg²⁺ and the resultant Mg⁺• can abstract a hydroxyl group from the glycan moiety to form a carbon radical. Subsequent radical migration and α-cleavage(s) result in the formation of a variety of product ions. The proposed hydroxyl abstraction mechanism correlates well with the major features in the ECD spectrum of the Mg²⁺-adducted cellohexaose. The mechanism presented here also predicts the presence of secondary, radical-induced fragmentation pathways. These secondary fragment ions could be misinterpreted, leading to erroneous structural determination. The present study highlights an urgent need for continuing investigation of the glycan ECD mechanism, which is imperative for successful development of bioinformatics tools that can take advantage of the rich structural information provided by ECD of metal-adducted glycans.

Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids

The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.

Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry

The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

Photodissociation of charge tagged peptides

Tris(2,4,6-trimethoxyphenyl) phosphonium acetyl (TMPP-Ac) was previously introduced to improve the mass spectrometric sequence analysis of peptides by fixing a permanent charge at the N-termini. However, peptides containing arginine residues did not fragment efficiently after TMPP-Ac modification. In this work, we combine charge derivatization with photodissociation. The fragmentation of TMPP-derivatized peptides is greatly improved and a series of N-terminal fragments is generated with complete sequence information. Arginine has a special effect on the fragmentation of the TMPP tagged peptides when it is the N-terminal peptide residue. Theoretical and experimental results suggest that this is due to hydrogen transfer from the charged N-terminus to the hydrogen-deficient peptide sequence.

Tunable charge tags for electron-based methods of peptide sequencing: design and applications

Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixed-charge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal c-type fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for N-terminal tagging of Arg-containing tryptic peptides.

The early life of a peptide cation-radical. Ground and excited-state trajectories of electron-based peptide dissociations during the first 330 femtoseconds

We report a new approach to investigating the mechanisms of fast peptide cation-radical dissociations based on an analysis of time-resolved reaction progress by Ehrenfest dynamics, as applied to an Ala-Arg cation-radical model system. Calculations of stationary points on the ground electronic state that were carried out with effective CCSD(T)/6-311++G(3df,2p) could not explain the experimental branching ratios for loss of a hydrogen atom, ammonia, and N-C(α) bond dissociation in (AR + 2H)(+•). The Ehrenfest dynamics results indicate that the ground and low-lying excited electronic states of (AR + 2H)(+•) follow different reaction courses in the first 330 femtoseconds after electron attachment. The ground (X) state undergoes competing loss of N-terminal ammonia and isomerization to an aminoketyl radical intermediate that depend on the vibrational energy of the charge-reduced ion. The A and B excited states involve electron capture in the Arg guanidine and carboxyl groups and are non-reactive on the short time scale. The C state is dissociative and progresses to a fast loss of an H atom from the Arg guanidine group. Analogous results were obtained by using the B3LYP and CAM-B3LYP density functionals for the excited state dynamics and including the universal M06-2X functional for ground electronic state calculations. The results of this Ehrenfest dynamics study indicate that reaction pathway branching into the various dissociation channels occurs in the early stages of electron attachment and is primarily determined by the electronic states being accessed. This represents a new paradigm for the discussion of peptide dissociations in electron based methods of mass spectrometry.

Dissociation channel dependence on peptide size observed in electron capture dissociation of tryptic peptides

Electron capture dissociation (ECD) of a series of five residue peptides led to the observation that these small peptides did not lead to the formation of the usual c/z ECD fragments, but to a, b, y, and w fragments. In order to determine how general this behavior is for small sized peptides, the effect of peptide size on ECD fragments using a complete set of ECD spectra from the SwedECD spectra database was examined. Analysis of the database shows that b and w fragments are favored for small peptide sizes and that average fragment size shows a linear relationship to parent peptide size for most fragment types. From these data, it appears that most of the w fragments are not secondary fragments of the major z ions, in sharp contrast with the proposed mechanism leading to these ions. These data also show that c fragment distributions depend strongly on the nature of C-terminal residue basic site: arginine leads to loss of short neutral fragments, whereas lysine leads to loss of longer neutral fragments. It also appears that b ions might be produced by two different mechanisms depending on the parent peptide size. A model for the fragmentation pathways in competition is proposed. These relationships between average fragment size and parent peptide size could be further exploited also for CID fragment spectra and could be included in fragmentation prediction algorithms.

Tandem MS analysis of selenamide-derivatized peptide ions

Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen (m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

Formation of peptide radical cations (m+·) in electron capture dissociation of peptides adducted with group IIB metal ions

Peptides adducted with different divalent Group IIB metal ions (Zn(2+), Cd(2+), and Hg(2+)) were found to give very different ECD mass spectra. ECD of Zn(2+) adducted peptides gave series of c-/z-type fragment ions with and without metal ions. ECD of Cd(2+) and Hg(2+) adducted model peptides gave mostly a-type fragment ions with M(+•) and fragment ions corresponding to losses of neutral side chain from M(+•). No detectable a-ions could be observed in ECD spectra of Zn(2+) adducted peptides. We rationalized the present findings by invoking both proton-electron recombination and metal-ion reduction processes. As previously postulated, divalent metal-ions adducted peptides could adopt several forms, including (a) [M + Cat](2+), (b) [(M + Cat - H) + H](2+), and (c) [(M + Cat - 2H) + 2H](2+). The relative population of these precursor ions depends largely on the acidity of the metal-ion peptide complexes. Peptides adducted with divalent metal-ions of small ionic radii (i.e., Zn(2+)) would form predominantly species (b) and (c); whereas peptides adducted with metal ions of larger ionic radii (i.e., Hg(2+)) would adopt predominantly species (a). Species (b) and (c) are believed to be essential for proton-electron recombination process to give c-/z-type fragments via the labile ketylamino radical intermediates. Species (c) is particularly important for the formation of non-metalated c-/z-type fragments. Without any mobile protons, species (a) are believed to undergo metal ion reduction and subsequently induce spontaneous electron transfer from the peptide moiety to the charge-reduced metal ions. Depending on the exothermicity of the electron transfer reaction, the peptide radical cations might be formed with substantial internal energy and might undergo further dissociation to give structural related fragment ions.

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.

The histidine effect. Electron transfer and capture cause different dissociations and rearrangements of histidine peptide cation-radicals

Electron-transfer and -capture dissociations of doubly protonated peptides gave dramatically different product ions for a series of histidine-containing pentapeptides of both non-tryptic (AAHAL, AHAAL, AHADL, AHDAL) and tryptic (AAAHK, AAHAK, AHAAK, HAAAK, AAAHR, AAHAR, AHAAR, HAAAR) type. Electron transfer from gaseous Cs atoms and fluoranthene anions triggered backbone dissociations of all four N-C(alpha) bonds in the peptide ions in addition to loss of H and NH(3). Substantial fractions of charge-reduced cation-radicals did not dissociate on an experimental time scale ranging from 10(-6) to 10(-1) s. Multistage tandem mass spectrometric (MS(n)) experiments indicated that the non-dissociating cation-radicals had undergone rearrangements. These were explained as being due to proton migrations from N-terminal ammonium and COOH groups to the C-2' position of the reduced His ring, resulting in substantial radical stabilization. Ab initio calculations revealed that the charge-reduced cation-radicals can exist as low-energy zwitterionic amide pi* states which were local energy minima. These states underwent facile exothermic proton migrations to form aminoketyl radical intermediates, whereas direct N-C(alpha) bond cleavage in zwitterions was disfavored. RRKM analysis indicated that backbone N-C(alpha) bond cleavages did not occur competitively from a single charge-reduced precursor. Rather, these bond cleavages proceeded from distinct intermediates which originated from different electronic states accessed by electron transfer. In stark contrast to electron transfer, capture of a free electron by the peptide ions mainly induced radical dissociations of the charge-carrying side chains and loss of a hydrogen atom followed by standard backbone dissociations of even-electron ions. The differences in dissociation are explained by different electronic states being accessed upon electron transfer and capture.

Probing the mechanisms of electron capture dissociation mass spectrometry with nitrated peptides

Previously we have shown that the presence of 3-nitrotyrosine within a peptide sequence severely depletes the peptide backbone fragments typically observed following electron capture dissociation (ECD) mass spectrometry. Instead, ECD of nitrated peptides is characterised by abundant losses of small neutrals (hydroxyl radicals, water and ammonia). Here, we investigate the origin of ammonia loss by comparing the ECD behaviour of lysine- and arginine-containing nitrated peptides, and their N-acetylated counterparts, and nitrated peptides containing no basic amino acid residues. The results reveal that ammonia loss derives from the N-terminus of the peptides, however, the key finding of this work is the insight provided into the hierarchy of various proposed ECD mechanisms: the Utah-Washington mechanism, the electron predator mechanism and the Oslo mechanism.

Electron predators are hydrogen atom traps. Effects of aryl groups on N-C(α) bond dissociations of peptide radicals

Effects of substituted aryl groups on dissociations of peptide aminoketyl radicals were studied computationally for model tetrapeptide intermediates GXD(•) G where X was a cysteine residue that was derivatized by S-(3-nitrobenzyl), S-(3-cyanobenzyl), S-(3,5-dicyanobenzyl), S-(2,3,4,5,6-pentafluorobenzyl), and S-benzyl groups. The aminoketyl radical was placed within the Asp amide group. Aminoketyl radicals having the S-(3-nitrobenzyl) group were found to undergo spontaneous and highly exothermic migration of the hydroxyl hydrogen atom onto the nitro group in conformers allowing interaction between these groups. Competing reaction channels were investigated for aminoketyl radicals having the S-(3-cyanobenzyl) and S-(3,5-dicyanobenzyl) groups, e.g. H-atom migration to the C and N atoms of the C≡N group, migration to the C-4 position of the phenyl ring, and dissociation of the radical-activated NC(α) bond between the Asp and Gly residues. RRKM kinetic analysis on the combined B3LYP and ROMP2/6-311++G(2d,p) potential energy surface indicated > 99% H-atom transfer to the C≡N group forming a stable iminyl intermediate. The NC(α) bond dissociation was negligible. In contrast, peptides with the S-(2,3,4,5,6-pentafluorobenzyl) and S-benzyl groups showed preferential NC(α) bond dissociation that outcompeted H-atom migration to the C-4 position and fluorine substituents in the phenyl ring. These computational results are used to suggest an alternative mechanism for the quenching effect on electron-based peptide backbone dissociations of benzyl groups with electron-withdrawing substitutents, as reported recently.

Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation

Mass spectrometry analysis of protein-nucleic acid cross-links is challenging due to the dramatically different chemical properties of the two components. Identifying specific sites of attachment between proteins and nucleic acids requires methods that enable sequencing of both the peptide and oligonucleotide component of the heteroconjugate cross-link. While collision-induced dissociation (CID) has previously been used for sequencing such heteroconjugates, CID generates fragmentation along the phosphodiester backbone of the oligonucleotide preferentially. The result is a reduction in peptide fragmentation within the heteroconjugate. In this work, we have examined the effectiveness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) for sequencing heteroconjugates. Both methods were found to yield preferential fragmentation of the peptide component of a peptide:oligonucleotide heteroconjugate, with minimal differences in sequence coverage between these two electron-induced dissociation methods. Sequence coverage was found to increase with increasing charge state of the heteroconjugate, but decreases with increasing size of the oligonucleotide component. To overcome potential intermolecular interactions between the two components of the heteroconjugate, supplemental activation with ETD was explored. The addition of a supplemental activation step was found to increase peptide sequence coverage over ETD alone, suggesting that electrostatic interactions between the peptide and oligonucleotide components are one limiting factor in sequence coverage by these two approaches. These results show that ECD/ETD methods can be used for the tandem mass spectrometry sequencing of peptide:oligonucleotide heteroconjugates, and these methods are complementary to existing CID methods already used for sequencing of protein-nucleic acid cross-links.

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Series of doubly and triply protonated diarginated peptide molecules with different number of glutamic acid (E) and asparagine (N) residues were analyzed under ECD conditions. ECD spectra of doubly-protonated peptides show a strong dependence on the number of E and N residues. Both the backbone cleavages and hydrogen radical (H*) loss from the charge-reduced precursor ions ([M+2H](+*)) were suppressed as the number of E and N residues increases. A strong inhibition of the backbone cleavages and H* loss from [M+2H](+*) was found for peptides with 6E residues (or 4E + 2N residues). The results obtained using these model peptides were re-confirmed by analyzing N-arginated Fibrinopeptide-B (i.e., REGVNDNEEGFFSAR). In contrast to the N-arginated peptide, ECD of the doubly-protonated Fibrinopeptide-B and its analogues show extensive backbone cleavages leading to series of c- and z-ions ( approximately 80% sequence coverage). Based on these results, it is believed that peptide ions with all surplus protons sequestered in arginine-residues would show enhanced stability under ECD conditions as the number of acid-residue increases. The suppression of backbone cleavages and H* loss from [M+2H](+*) are presumably attributed to the low reactivity of the charge-reduced precursor ions. One of the possible hypothesis is that diarginated E-rich peptides may contain hydrogen bonds between carbonyl oxygen of E side chains and backbone amide hydrogen. These hydrogen bonds would provide extra stabilization for [M+2H](+*). This is the first demonstration of natural structural motifs in peptides that would inhibit the backbone fragmentation of the charge-reduced peptide ions under ECD conditions.

Measuring the extent and width of internal energy deposition in ion activation using nanocalorimetry

The recombination energies resulting from electron capture by a positive ion can be accurately measured using hydrated ion nanocalorimetry in which the internal energy deposition is obtained from the number of water molecules lost from the reduced cluster. The width of the product ion distribution in these experiments is predominantly attributable to the distribution of energy that partitions into the translational and rotational modes of the water molecules that are lost. These results are consistent with a singular value for the recombination energy. For large clusters, the width of the energy distribution is consistent with rapid energy partitioning into internal vibrational modes. For some smaller clusters with high recombination energies, the measured product ion distribution is narrower than that calculated with a statistical model. These results indicate that initial water molecule loss occurs on the time scale of, or faster than energy randomization. This could be due to inherently slow internal conversion or it could be due to a multi-step process, such as initial ion-electron pair formation followed by reduction of the ion in the cluster. These results provide additional evidence for the accuracy with which condensed phase thermochemical values can be deduced from gaseous nanocalorimetry experiments.

Enhanced electron transfer dissociation through fixed charge derivatization of cysteines

Electron transfer dissociation (ETD) has proven to be a promising new ion activation method for proteomics applications due to its ability to generate c- and z-type fragment ions in comparison to the y- and b-type ions produced upon the more conventional collisional activation of peptides. However, low precursor charge states hinder the success of electron-based activation methods due to competition from nondissociative charge reduction and incomplete sequence coverage. In the present report, the reduction and alkylation of disulfide bonds prior to ETD analysis is evaluated by comparison of three derivatization reagents: iodoacetamide (IAM), N,N-dimethyl-2-chloro-ethylamine (DML), and (3-acrylamidopropyl)-trimethyl ammonium chloride (APTA). While both the DML and APTA modifications lead to an increase in the charge states of peptides, the APTA-peptides provided the most significant improvement in percent fragmentation and sequence coverage for all peptides upon ETD, including formation of diagnostic ions that allow characterization of both the C- and N-termini. In addition, the formation of product ions in multiple charge states upon ETD is minimized for the APTA-modified peptides.

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.

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.

Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools

This tutorial provides an overview of the evolution of some of the key concepts in the gas-phase fragmentation of different classes of peptide ions under various conditions [e.g. collision-induced dissociation (CID) and electron transfer dissociation (ETD)], and then demonstrates how these concepts can be used to develop new methods. For example, an understanding of the role of the mobile proton and neighboring group interactions in the fragmentation reactions of protonated peptides has led to the design of the 'SELECT' method. For ETD, a model based on the Landau-Zener theory reveals the role of both thermodynamic and geometric effects in the electron transfer from polyatomic reagent anions to multiply protonated peptides, and this predictive model has facilitated the design of a new strategy to form ETD reagent anions from precursors generated via ESI. Finally, two promising, emerging areas of gas-phase ion chemistry of peptides are also described: (1) the design of new gas-phase radical chemistry to probe peptide structure, and (2) selective cleavage of disulfide bonds of peptides in the gas phase via various physicochemical approaches.

The effect of fixed charge modifications on electron capture dissociation

Electron capture dissociation (ECD) studies of two modified amyloid beta peptides (20-29 and 25-35) were performed to investigate the role of H* radicals in the ECD of peptide ions and the free-radical cascade (FRC) mechanism. 2,4,6-Trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H* generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller abundance decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the nonprotonated nature of all charge carriers in doubly labeled peptide ions, several c and z* ions were still observed in their ECD spectra. Thus, although H* transfer may be important for the NC(alpha) bond cleavage, there also exist other pathways, which would require a radical migration via H* abstraction through space or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.

Electron transfer dissociation of iTRAQ labeled peptide ions

Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD and supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/ z 162 yielded the reporter ion at m/ z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents.

The effect of phosphorylation on the electron capture dissociation of peptide ions

The effect of site and frequency of phosphorylation on the electron capture dissociation of peptide ions has been investigated. The ECD of a suite of synthetic peptides (APLSFRGSLPKSYVK; one unmodified, three singly-phosphorylated, three-doubly phosphorylated, and one triply-phosphorylated); two tryptic phosphopeptides (YKVPQLEIVPN(p)SAEER, alpha-casein and FQ(p)SEEQQQTEDELQDK, beta-casein) and their unmodified counterparts, were determined over a range of ECD cathode potentials. The results show that, for doubly-charged precursor ions, the presence of phosphorylation has a deleterious effect on ECD sequence coverage. The fragmentation patterns observed suggest that for peptides with multiple basic residues, the phospho-groups exist in their deprotonated form and form salt-bridges with protonated amino acid side chains. The fragmentation observed for the acidic tryptic peptides suggested the presence of noncovalent interactions, which were perturbed on phosphorylation. Increasing the ECD electron energy significantly improves sequence coverage. Alternatively, improved sequence coverage can be achieved by performing ECD on triply-charged precursor ions. The findings are important for the understanding of gas-phase fragmentation of phosphopeptides.

Electron capture by a hydrated gaseous peptide: effects of water on fragmentation and molecular survival

The effects of water on electron capture dissociation products, molecular survival, and recombination energy are investigated for diprotonated Lys-Tyr-Lys solvated by between zero and 25 water molecules. For peptide ions with between 12 and 25 water molecules attached, electron capture results in a narrow distribution of product ions corresponding to primarily the loss of 10-12 water molecules from the reduced precursor. From these data, the recombination energy (RE) is determined to be equal to the energy that is lost by evaporating on average 10.7 water molecules, or 4.3 eV. Because water stabilizes ions, this value is a lower limit to the RE of the unsolvated ion, but it indicates that the majority of the available RE is deposited into internal modes of the peptide ion. Plotting the fragment ion abundances for ions formed from precursors with fewer than 11 water molecules as a function of hydration extent results in an energy resolved breakdown curve from which the appearance energies of the b 2 (+), y 2 (+), z 2 (+*), c 2 (+), and (KYK + H) (+) fragment ions formed from this peptide ion can be obtained; these values are 78, 88, 42, 11, and 9 kcal/mol, respectively. The propensity for H atom loss and ammonia loss from the precursor changes dramatically with the extent of hydration, and this change in reactivity can be directly attributed to a "caging" effect by the water molecules. These are the first experimental measurements of the RE and appearance energies of fragment ions due to electron capture dissociation of a multiply charged peptide. This novel ion nanocalorimetry technique can be applied more generally to other exothermic reactions that are not readily accessible to investigation by more conventional thermochemical methods.

Electronic properties of charge-tagged peptides upon electron capture

We report a computational study of Ala-Lys (AK) and Lys-Ala (KA) dipeptide ions furnished with fixed-charged pyridinium groups that were attached by amide linkers to the N-terminal amino groups. Cation-radicals from one-electron reduction of the doubly charged AK and KA peptide conjugates showed various extents of unpaired electron density being delocalized between the pyridine and peptide moieties. The delocalization depended on the local recombination energies (RE(loc)) of the charged groups. The RE(loc) of the pyridine moieties were modified by introducing electron-donating substituents (CH(3), OCH(3), and N(CH(3))(2)). The RE(loc) of the peptide moieties were found to depend on the peptide conformation and internal solvation of the Lys ammonium groups. Substantial electron delocalization was found for combinations of pyridine substituents and peptide conformers with closely matched RE(loc), such as 4-dimethylamino-pyridine and internally solvated Lys ammonium or unsubstituted pyridine and free (unsolvated) Lys ammonium. The dissociation (DeltaH(diss)) and transition state energies (E(TS)) for the loss of the pyridine ring from the conjugates were found to be DeltaH(diss) = 34-36 kJ mol(-1) and E(TS) = 67-69 kJ mol(-1) for the unsubstituted pyridine moieties, but did not depend much on the peptide sequence.