Tracking radical migration in large hydrogen deficient peptides with covalent labels: facile movement does not equal indiscriminate fragmentation

Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry

We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol^-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol^-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.

Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics

Ion-ion reactions are valuable tools in mass-spectrometry-based peptide and protein sequencing. To boost the generation of sequence-informative fragment ions from low charge-density precursors, supplemental activation methods, via vibrational and photoactivation, have become widely adopted. However, long-lived radical peptide cations undergo intramolecular hydrogen atom transfer from c-type ions to z^•-type ions. Here we investigate the degree of hydrogen transfer for thousands of unique peptide cations where electron transfer dissociation (ETD) was performed and was followed by beam-type collisional activation (EThcD), resonant collisional activation (ETcaD), or concurrent infrared photoirradiation (AI-ETD). We report on the precursor charge density and the local amino acid environment surrounding bond cleavage to illustrate the effects of intramolecular hydrogen atom transfer for various precursor ions. Over 30% of fragments from EThcD spectra comprise distorted isotopic distributions, whereas over 20% of fragments from ETcaD have distorted distributions and less than 15% of fragments derived from ETD and AI-ETD reveal distorted isotopic distributions. Both ETcaD and EThcD give a relatively high degree of hydrogen migration, especially when D, G, N, S, and T residues were directly C-terminal to the cleavage site. Whereas all postactivation methods boost the number of c- and z^•-type fragment ions detected, the collision-based approaches produce higher rates of hydrogen migration, yielding fewer spectral identifications when only c- and z^•-type ions are considered. Understanding hydrogen rearrangement between c- and z^•-type ions will facilitate better spectral interpretation.

Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules

The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.

Multiple Hydrogen Loss from [M + H]+ and [a]+ ions of Peptides in MALDI In-Source Decay Using a Dinitro-Substituted Matrix

The formation and radical-directed dissociation of multiple hydrogen-abstracted peptide cations [M + H - mH]·⁺ has been reported using MALDI-ISD with dinitro-substituted matrices. The MALDI-ISD of synthetic peptides using 3,5-dinitrosalicylic acid (3,5-DNSA) and 3,4-dinitrobenzoic acid (3,4-DNBA) as matrices resulted in multiple hydrogen abstraction from the analyte [M + H]⁺ and fragment [a]⁺ ions, i.e., [M + H - mH]⁺ and [a - mH]⁺ (m = 1-8). All of the ISD spectra showed unusually intense [a]⁺ ions originating from cleavage at the Cα-C bond of the Leu-Xxx residues when peptides without Phe/Tyr/His/Cys residues were used. The intensity of the [a_n]⁺ series ions generated using 3,5-DNSA and 3,4-DNBA rapidly decreased with increasing residue number n, suggesting cleavage at multiradical sites of [M + H - mH]^•+. It was suggested that multiple hydrogen abstraction from protonated peptides [M + H]⁺ mainly takes place from the backbone amide nitrogen.

Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis

Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.

Investigation of the position of the radical in z3-ions resulting from electron transfer dissociation using infrared ion spectroscopy

The molecular structures of six open-shell z₃-ions resulting from electron transfer dissociation mass spectrometry (ETD MS) were investigated using infrared ion spectroscopy in combination with density functional theory and molecular mechanics/molecular dynamics calculations.

Specific Cα-C Bond Cleavage of β-Carbon-Centered Radical Peptides Produced by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Radical-driven dissociation (RDD) of hydrogen-deficient peptide ions [M - H + H]^·+ has been examined using matrix-assisted laser dissociation/ionization in-source decay mass spectrometry (MALDI-ISD MS) with the hydrogen-abstracting matrices 4-nitro-1-naphthol (4,1-NNL) and 5-nitrosalicylic acid (5-NSA). The preferential fragment ions observed in the ISD spectra include N-terminal [a] + ions and C-terminal [x]⁺, [y + 2]⁺, and [w]⁺ ions which imply that β-carbon (Cβ)-centered radical peptide ions [M - Hβ + H]^·+ are predominantly produced in MALDI conditions. RDD reactions from the peptide ions [M - Hβ + H]^·+ successfully explains the fact that both [a]⁺ and [x]⁺ ions arising from cleavage at the Cα-C bond of the backbone of Gly-Xxx residues are missing from the ISD spectra. Furthermore, the formation of [a]⁺ ions originating from the cleavage of Cα-C bond of deuterated Ala(d3)-Xxx residues indicates that the [a]⁺ ions are produced from the peptide ions [M - Hβ + H]^·+ generated by deuteron-abstraction from Ala(d3) residues. It is suggested that from the standpoint of hydrogen abstraction via direct interactions between the nitro group of matrix and hydrogen of peptides, the generation of the peptide radical ions [M - Hβ + H]^·+ is more favorable than that of the α-carbon (Cα)-centered radical ions [M - Hα + H]^·+ and the amide nitrogen-centered radical ions [M - H_N + H]^·+, while ab initio calculations indicate that the formation of [M - Hα + H]^·+ is energetically most favorable. Graphical Abstract ᅟ.

Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis

Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers. Graphical Abstract ᅟ.

Isomerization versus dissociation of phenylalanylglycyltryptophan radical cations

Four isomers of the radical cation of tripeptide phenylalanylglycyltryptophan, in which the initial location of the radical center is well defined, have been isolated and their collision-induced dissociation (CID) spectra examined. These ions, the π-centered [FGW_π˙]⁺, α-carbon- [FG_α˙W]⁺, N-centered [FGW_N˙]⁺ and ζ-carbon- [F_ζ˙GW]⁺ radical cations, were generated via collision-induced dissociation (CID) of transition metal-ligand-peptide complexes, side chain fragmentation of a π-centered radical cation, homolytic cleavage of a labile nitrogen-nitrogen single bond, and laser induced dissociation of an iodinated peptide, respectively. The π-centered and tryptophan N-centered peptide radical cations produced almost identical CID spectra, despite the different locations of their initial radical sites, which indicated that interconversion between the π-centered and tryptophan N-centered radical cations is facile. By contrast, the α-carbon-glycyl radical [FG_α˙W]⁺, and ζ-phenyl radical [F_ζ˙GW]⁺, featured different dissociation product ions, suggesting that the interconversions among α-carbon, π-centered (or tryptophan N-centered) and ζ-carbon-radical cations have higher barriers than those to dissociation. Density functional theory calculations have been used to perform systematic mechanistic investigations on the interconversions between these isomers and to study selected fragmentation pathways for these isomeric peptide radical cations. The results showed that the energy barrier for interconversion between [FGW_π˙]⁺ and [FGW_N˙]⁺ is only 31.1 kcal mol^-1, much lower than the barriers to their dissociation (40.3 kcal mol^-1). For the [FGW_π˙]⁺, [FG_α˙W]⁺, and [F_ζ˙GW]⁺, the barriers to interconversion are higher than those to dissociation, suggesting that interconversions among these isomers are not competitive with dissociations. The [z₃ - H]˙⁺ ions isolated from [FG_α˙W]⁺ and [F_ζ˙GW]⁺ show distinctly different fragmentation patterns, indicating that the structures of these ions are different and this result is supported by the DFT calculations.

TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research. Graphical Abstract ᅟ.

Structural Effects of Solvation by 18-Crown-6 on Gaseous Peptides and TrpCage after Electrospray Ionization

Significant effort is being employed to utilize the inherent speed and sensitivity of mass spectrometry for rapid structural determination of proteins; however, a thorough understanding of factors influencing the transition from solution to gas phase is critical for correct interpretation of the results from such experiments. It was previously shown that combined use of action excitation energy transfer (EET) and simulated annealing can reveal detailed structural information about gaseous peptide ions. Herein, we utilize this method to study microsolvation of charged groups by retention of 18-crown-6 (18C6) in the gas phase. In the case of GTP (CEGNVRVSRE LAGHTGY), solvation of the 2+ charge state leads to reduced EET, whereas the opposite result is obtained for the 3+ ion. For the mini-protein C-Trpcage, solvation by 18C6 leads to dramatic increase in EET for the 3+ ion. Examination of structural details probed by molecular dynamics calculations illustrate that solvation by 18C6 alleviates the tendency of charged side chains to seek intramolecular solvation, potentially preserving native-like structures in the gas phase. These results suggest that microsolvation may be an important tool for facilitating examination of native-like protein structures in gas phase experiments. Graphical Abstract ᅟ.

Radical-induced dissociation leading to the loss of CO2 from the oxazolone ring of [b5- H]˙(+) ions

Macrocyclization is commonly observed in large bn(+) (n≥ 4) ions and as a consequence can lead to incorrect protein identification due to sequence scrambling. In this work, the analogous [b5- H]˙(+) radical cations derived from aliphatic hexapeptides (GA5˙(+)) also showed evidence of macrocyclization under CID conditions. However, the major fragmentation for [b5- H]˙(+) ions is the loss of CO2 and not CO loss, which is commonly observed in closed-shell bn(+) ions. Isotopic labeling using CD3 and (18)O revealed that more than one common structure underwent dissociations. Theoretical studies found that the loss of CO2 is radical-driven and is facilitated by the radical being located at the Cα atom immediately adjacent to the oxazolone ring. Comparable energy barriers against macrocyclization, hydrogen-atom transfer, and fragmentations are found by DFT calculations and the results are consistent with the experimental observations that a variety of dissociation products are observed in the CID spectra.

Nucleophilic substitution by amide nitrogen in the aromatic rings of [zn - H]˙⁺ ions; the structures of the [b₂ - H - 17]˙⁺ and [c1 - 17]⁺ ions

Peptide radical cations that contain an aromatic amino acid residue cleave to give [zn - H]˙⁺ ions with [b2 - H - 17]˙⁺ and [c1 - 17](+) ions, the dominant products in the dissociation of [zn - H]˙⁺, also present in lower abundance in the CID spectra. Isotopic labeling in the aromatic ring of [Yπ˙GG](+) establishes that in the formation of [b2 - H - 17]˙⁺ ions a hydrogen from the δ-position of the Y residue is lost, indicating that nucleophilic substitution on the aromatic ring has occurred. A preliminary DFT investigation of nine plausible structures for the [c1 - 17](+) ion derived from [Y(π)˙GG](+) shows that two structures resulting from attack on the aromatic ring by oxygen and nitrogen atoms from the peptide backbone have significantly better energies than other isomers. A detailed study of [Y(π)˙GG](+) using two density functionals, B3LYP and M06-2X, with a 6-31++G(d,p) basis set gives a higher barrier for attack on the aromatic ring of the [zn - H]˙⁺ ion by nitrogen than by the carbonyl oxygen. However, subsequent rearrangements involving proton transfers are much higher in energy for the oxygen-substituted isomer leading to the conclusion that the [c1 - 17](+) ions are the products of nucleophilic attack by nitrogen, protonated 2,7-dihydroxyquinoline ions. The [b2 - H - 17]˙⁺ ions are formed by loss of glycine from the same intermediates involved in the formation of the [c1 - 17](+) ions.

Theoretical examination of competitive β-radical-induced cleavages of N–Cα and Cα–C bonds of peptides

Selective cleavages of N–Cα and Cα–C bonds of β-radical tautomers of amino acid residues in radical peptides have been examined theoretically by means of the density functional theory at the M06-2X/6-311++G(d,p) level. The majority of the bond cleavages are homolytic via β-scission. Their energy barriers depend largely on the ability of the radical being stabilized in the transition structures and the availability of a mobile proton in the vicinity of the β-radical center. The N–Cα bond is less favorably cleaved than the Cα–C bond (except Ser and Thr) for systems without a mobile proton. It is because, firstly, the homolytic cleavage is less favorable for the more polar N–Cα bond than for the less polar Cα–C bond. Secondly, a less stable σ-radical localized on the amide nitrogen atom of the incipient N-terminal fragment is formed for the former, while a more stable radical delocalized in a π*(CO)-like orbital of the incipient C-terminal fragment is formed for the latter. In the presence of a mobile proton N-terminal to the β-radical center, some degrees of heterolytic cleavage character, as preferred by the polar N–Cα bond, are observed. Consequently, its barrier is reduced. If the mobile proton is located at the C-terminal amide oxygen of the β-radical center, the Cα–C bond cleavage will be significantly suppressed. It is because the radical in the incipient C-terminal fragment becomes more localized as a σ-radical on the carbon atom of its protonated amide group. With basic amino acid residues, the Cα–C bond cleavage can be reactivated. Heterolytic cleavage of the polar N–Cα bond can be largely facilitated if a mobile proton N-terminal to the β-radical center is available and the radical in the incipient C-terminal fragment is sufficiently stabilized, for instance, by the aromatic side chain of Trp and Tyr. Therefore, cleavages of the N–Cα bond induced by the β-radical tautomer of Trp and Tyr are often preferred as compared with cleavages of the Cα–C bond in peptide radical cations containing mobile protons.

Radical-induced, proton-transfer-driven fragmentations in [b(5)-H]˙(+) ions derived from pentaalanyl tryptophan

The collision-induced dissociation (CID) of [b5 - H]˙(+) ions containing four alanine residues and one tryptophan give identical spectra regardless of the initial location of the tryptophan indicating that, as proposed for b5(+) ions, sequence scrambling occurs prior to dissociation. Cleavage occurs predominantly at the peptide bonds and at the N-Cα bond of the alanine residue that is attached to the N-terminus of the tryptophan residue. The product of the latter pathway, an ion at m/z 240, is the base peak in all the mass spectra. With the exception of one minor channel giving a b3(+) ion, the product ions retain both the tryptophan residue and the radical. Experiments with one trideuterated alanine established the sequences of loss of alanine residues. Formation of identical products implies a common intermediate, a [b5 - H]˙(+) ion that has a 'linear' structure in which the tryptophan residue is present as an α-radical located in the oxazolone ring, structure Ie. Density functional theory calculations show this structure to be at the global minimum, 14.6 kcal mol(-1) below the macrocyclic structure, ion II. Loss of CO from the [b5 - H]˙(+) ions is inhibited by the presence of the radical centre in the oxazolone ring and migration of the proton from the oxazolone ring onto the peptide backbone induces cleavage of an N-Cα or peptide bond. Three calculated structures for the ion at m/z 240 all have an oxazolone ring. Two of these structures may be formed from Ie, depending upon which proton migrates onto the peptide chain prior to the dissociation. The barrier to interconversion between these two structures requires a 1,3-hydrogen atom shift and is high (51.0 kcal mol(-1)), but both can convert into a third isomer that readily loses CO2 (barrier 38.7 kcal mol(-1)). The lowest barrier to the loss of CO, the usual fragmentation path observed for protonated oxazolones, is 47.0 kcal mol(-1).

Radical-driven peptide backbone dissociation tandem mass spectrometry

In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach.

Dissociation behavior of a bifunctional tempo-active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry

We have synthesized a homobifunctional active ester cross-linking reagent containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) moiety connected to a benzyl group (Bz), termed TEMPO-Bz-linker. The aim for designing this novel cross-linker was to facilitate MS analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO-Bz-linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof-of-principle study was to evaluate the potential of the TEMPO-Bz-linker for chemical cross-linking studies to derive 3D-structure information of proteins. Our studies were motivated by the well documented instability of the central NO-C bond of TEMPO-Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO-C bond of the TEMPO-Bz-linker. This leads to the formation of complementary open-shell peptide radical cations, while precursor ions that are protonated at the TEMPO-Bz-linker itself exhibit a charge-driven formation of even-electron product ions upon collision activation. MS(3) product ion experiments provided amino acid sequence information and allowed determining the cross-linking site. Our study fully characterizes the CID behavior of the TEMPO-Bz-linker and demonstrates its potential, but also its limitations for chemical cross-linking applications utilizing the special features of open-shell peptide ions on the basis of selective tandem MS analysis.

Surface-induced dissociation: a unique tool for studying energetics and kinetics of the gas-phase fragmentation of large ions

Surface-induced dissociation (SID) is a valuable tool for investigating the activation and dissociation of large ions in tandem mass spectrometry. This account summarizes key findings from studies of the energetics and mechanisms of complex ion dissociation in which SID experiments were combined with Rice-Ramsperger-Kassel-Marcus modeling of the experimental data. These studies used time- and collision-energy-resolved SID experiments and SID combined with resonant ejection of selected fragment ions on a specially designed Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Fast-ion activation by collision with a surface combined with the long and variable timescale of FT-ICR mass spectrometry is perfectly suited to studying the energetics and dynamics of complex ion dissociation in the gas phase. Modeling of time- and collision-energy-resolved SID enables the accurate determination of energy and entropy effects in the dissociation process. It has been demonstrated that entropy effects play an important role in determining the dissociation rates of both covalent and noncovalent bonds in large gaseous ions. SID studies have provided important insights on the competition between charge-directed and charge-remote fragmentation in even-electron peptide ions and the role of the charge and radical site on the energetics of the dissociation of odd-electron peptide ions. Furthermore, this work examined factors that affect the strength of noncovalent binding, as well as the competition between covalent and noncovalent bond cleavages and between proton and electron transfer in model systems. Finally, SID studies have been used to understand the factors affecting nucleation and growth of clusters in solution and in the gas phase.

Discovery and mechanistic studies of facile N-terminal Cα-C bond cleavages in the dissociation of tyrosine-containing peptide radical cations

Fascinating N-terminal Cα-C bond cleavages in a series of nonbasic tyrosine-containing peptide radical cations have been observed under low-energy collision-induced dissociation (CID), leading to the generation of rarely observed x-type radical fragments, with significant abundances. CID experiments of the radical cations of the alanyltyrosylglycine tripeptide and its analogues suggested that the N-terminal Cα-C bond cleavage, yielding its [x2 + H](•+) radical cation, does not involve an N-terminal α-carbon-centered radical. Theoretical examination of a prototypical radical cation of the alanyltyrosine dipeptide, using density functional theory calculations, suggested that direct N-terminal Cα-C bond cleavage could produce an ion-molecule complex formed between the incipient a1(+) and x1(•) fragments. Subsequent proton transfer from the iminium nitrogen atom in a1(+) to the acyl carbon atom in x1(•) results in the observable [x1 + H](•+). The barriers against this novel Cα-C bond cleavage and the competitive N-Cα bond cleavage, forming the complementary [c1 + 2H](+)/[z1 - H](•+) ion pair, are similar (ca. 16 kcal mol(-1)). Rice-Ramsperger-Kassel-Marcus modeling revealed that [x1 + H](•+) and [c1 + 2H](+) species are formed with comparable rates, in agreement with energy-resolved CID experiments for [AY](•+).

Formation, isomerization, and dissociation of ε- and α-carbon-centered tyrosylglycylglycine radical cations

The CID spectra of [Y^ε˙GG]⁺ and [YGG^α˙]⁺ are identical, showing that interconversion occurs prior to dissociation. For [Y^ε˙GG]⁺, [Y^π˙GG]⁺ and [YG^α˙G]⁺, the dissociation products are all distinctly different, indicating that dissociation occurs more readily than isomerization.

Activated ion negative electron transfer dissociation of multiply charged peptide anions

We report the implementation and evaluation of activated ion negative electron transfer dissociation (AI-NETD) in order to enhance the analytical capabilities of NETD for the elucidation of doubly deprotonated peptide anions. The analytical figures-of-merit and fragmentation characteristics are compared for NETD alone and with supplemental collisional activation of the charge reduced precursors or infrared photoactivation of the entire ion population during the NETD reaction period. The addition of supplemental collisional activation of charge reduced precursor ions or infrared photoactivation of the entire ion population concomitant with the NETD reaction period significantly improves sequencing capabilities for peptide anions as evidenced by the greater abundances of product ions and overall sequence coverage. Neither of these two AI-NETD methods significantly alters the net fragmentation efficiencies relative to NETD; however, the sequence ion conversion percentages with respect to formation of diagnostic product ions are notably higher. Supplemental infrared photoactivation outperforms collisional activation for most of the peptide fragmentation metrics evaluated.

Fragmentation chemistry of [Met-Gly]•+, [Gly-Met]•+, and [Met-Met]•+ radical cations

Radical cations [Met-Gly](•+), [Gly-Met](•+), and [Met-Met](•+) have been generated through collision-induced dissociation (CID) of [Cu(II)(CH3CN)2(peptide)](•2+) complexes. Their fragmentation patterns and dissociation mechanisms have been studied both experimentally and theoretically using density functional theory at the UB3LYP/6-311++G(d,p) level. The captodative structure, in which the radical is located at the α-carbon of the N-terminal residue and the proton is on the amide oxygen, is the lowest energy structure on each potential energy surface. The canonical structure, with the charge and spin both located on the sulfur, and the distonic ion with the proton on the terminal amino group, and the radical on the α-carbon of the C-terminal residue have similar energies. Interconversion between the canonical structures and the captodative isomers is facile and occurs prior to fragmentation. However, isomerization to produce the distonic structure is energetically less favorable and cannot compete with dissociation except in the case of [Gly-Met](•+). Charge-driven dissociations result in formation of [b(n) - H](•+) and a(1) ions. Radical-driven dissociation leads to the loss of the side chain of methionine as CH3-S-CH=CH2 producing α-glycyl radicals from both [Gly-Met](•+) and [Met-Met](•+). For [Met-Met](•+), loss of the side chain occurs at the C-terminal as shown by both labeling experiments and computations. The product, the distonic ion of [Met-Gly](•+), NH3 (+)CH(CH2CH2SCH3)CONHCH(•)COOH dissociates by loss of CH3S(•). The isomeric distonic ion NH3 (+)CH2CONHC(•)(CH2CH2SCH3)COOH is accessible directly from the canonical [Gly-Met](•+) ion. A fragmentation pathway that characterizes this ion (and the distonic ion of [Met-Met](•+)) is homolytic fission of the Cβ-Cγ bond to lose CH3SCH2(•).

Exploring radical migration pathways in peptides with positional isomers, deuterium labeling, and molecular dynamics simulations

One of the keys for understanding radical directed dissociation in peptides is a detailed knowledge of the factors that mediate radical migration. Peptide radicals can be created by a variety of means; however, in most circumstances, the originally created radicals must migrate to alternate locations in order to facilitate fragmentation such as backbone cleavage or side chain loss. The kinetics of radical migration are examined herein by comparing results from ortho-, meta-, and para-benzoyl radical positional isomers for several peptides. Isomers of a constrained cyclic peptide generated by several orthogonal radical initiators are also probed as a function of charge state. Cumulatively, the results suggest that small changes in radical position can significantly impact radical migration, and overall structural flexibility of the peptide is also an important controlling factor. A particularly interesting pathway for the peptide RGYALG that is sensitive to ortho versus meta or para substitution was fully mapped out by a suite of deuterium labeled peptides. This data was then used to optimize parameters in molecular dynamics-based simulations, which were subsequently used to obtain further insight into the structural underpinnings that most strongly influence the kinetics of radical migration.

Gas-phase peptide sulfinyl radical ions: formation and unimolecular dissociation

A variety of peptide sulfinyl radical (RSO•) ions with a well-defined radical site at the cysteine side chain were formed at atmospheric pressure (AP), sampled into a mass spectrometer, and investigated via collision-induced dissociation (CID). The radical ion formation was based on AP reactions between oxidative radicals and peptide ions containing single inter-chain disulfide bond or free thiol group generated from nanoelectrospray ionization (nanoESI). The radical induced reactions allowed large flexibility in forming peptide radical ions independent of ion polarity (protonated or deprotonated) or charge state (singly or multiply charged). More than 20 peptide sulfinyl radical ions in either positive or negative ion mode were subjected to low energy collisional activation on a triple-quadrupole/linear ion trap mass spectrometer. The competition between radical- and charge-directed fragmentation pathways was largely affected by the presence of mobile protons. For peptide sulfinyl radical ions with reduced proton mobility (i.e., singly protonated, containing basic amino acid residues), loss of 62 Da (CH(2)SO), a radical-initiated dissociation channel, was dominant. For systems with mobile protons, this channel was suppressed, while charge-directed amide bond cleavages were preferred. The polarity of charge was found to significantly alter the radical-initiated dissociation channels, which might be related to the difference in stability of the product ions in different ion charge polarities.

Electron capture dissociation of hydrogen-deficient peptide radical cations

Hydrogen-deficient peptide radical cations exhibit fascinating gas phase chemistry, which is governed by radical driven dissociation and, in many cases, by a combination of radical and charge driven fragmentation. Here we examine electron capture dissociation (ECD) of doubly, [M + H](2+•), and triply, [M + 2H](3+•), charged hydrogen-deficient species, aiming to investigate the effect of a hydrogen-deficient radical site on the ECD outcome and characterize the dissociation pathways of hydrogen-deficient species in ECD. ECD of [M + H](2+•) and [M + 2H](3+•) precursor ions resulted in efficient electron capture by the hydrogen-deficient species. However, the intensities of c- and z-type product ions were reduced, compared with those observed for the even electron species, indicating suppression of N-C(α) backbone bond cleavages. We postulate that radical recombination occurs after the initial electron capture event leading to a stable even electron intermediate, which does not trigger N-C(α) bond dissociations. Although the intensities of c- and z-type product ions were reduced, the number of backbone bond cleavages remained largely unaffected between the ECD spectra of the even electron and hydrogen-deficient species. We hypothesize that a small ion population exist as a biradical, which can trigger N-C(α) bond cleavages. Alternatively, radical recombination and N-C(α) bond cleavages can be in competition, with radical recombination being the dominant pathway and N-C(α) cleavages occurring to a lesser degree. Formation of b- and y-type ions observed for two of the hydrogen-deficient peptides examined is also discussed.

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.

Dissociation chemistry of hydrogen-deficient radical peptide anions

The fragmentation chemistry of anionic deprotonated hydrogen-deficient radical peptides is investigated. Homolytic photodissociation of carbon-iodine bonds with 266 nm light is used to generate the radical species, which are subsequently subjected to collisional activation to induce further dissociation. The charges do not play a central role in the fragmentation chemistry; hence deprotonated peptides that fragment via radical directed dissociation do so via mechanisms which have been reported previously for protonated peptides. However, charge polarity does influence the overall fragmentation of the peptide. For example, the absence of mobile protons favors radical directed dissociation for singly deprotonated peptides. Similarly, a favorable dissociation mechanism initiated at the N-terminus is more notable for anionic peptides where the N-terminus is not protonated (which inhibits the mechanism). In addition, collisional activation of the anionic peptides containing carbon-iodine bonds leads to homolytic cleavage and generation of the radical species, which is not observed for protonated peptides presumably due to competition from lower energy dissociation channels. Finally, for multiply deprotonated radical peptides, electron detachment becomes a competitive channel both during the initial photoactivation and following subsequent collisional activation of the radical. Possible mechanisms that might account for this novel collision-induced electron detachment are discussed.

Fragmentation of singly, doubly, and triply charged hydrogen deficient peptide radical cations in infrared multiphoton dissociation and electron induced dissociation

Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]((n+1)+·) (n=0, 1, 2), in MS(3) IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS(3) CID. Backbone fragmentation in MS(3) IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS(3) IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS(3) CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.

Novel Cβ-Cγ bond cleavages of tryptophan-containing peptide radical cations

In this study, we observed unprecedented cleavages of the C(β)-C(γ) bonds of tryptophan residue side chains in a series of hydrogen-deficient tryptophan-containing peptide radical cations (M(•+)) during low-energy collision-induced dissociation (CID). We used CID experiments and theoretical density functional theory (DFT) calculations to study the mechanism of this bond cleavage, which forms [M - 116](+) ions. The formation of an α-carbon radical intermediate at the tryptophan residue for the subsequent C(β)-C(γ) bond cleavage is analogous to that occurring at leucine residues, producing the same product ions; this hypothesis was supported by the identical product ion spectra of [LGGGH - 43](+) and [WGGGH - 116](+), obtained from the CID of [LGGGH](•+) and [WGGGH](•+), respectively. Elimination of the neutral 116-Da radical requires inevitable dehydrogenation of the indole nitrogen atom, leaving the radical centered formally on the indole nitrogen atom ([Ind](•)-2), in agreement with the CID data for [WGGGH](•+) and [W(1-CH3)GGGH](•+); replacing the tryptophan residue with a 1-methyltryptophan residue results in a change of the base peak from that arising from a neutral radical loss (116 Da) to that arising from a molecule loss (131 Da), both originating from C(β)-C(γ) bond cleavage. Hydrogen atom transfer or proton transfer to the γ-carbon atom of the tryptophan residue weakens the C(β)-C(γ) bond and, therefore, decreases the dissociation energy barrier dramatically.

Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H(2)PO(4) radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Site-selective fragmentation of peptides and proteins at quinone-modified cysteine residues investigated by ESI-MS

Described herein are several unique analytical applications utilizing mass spectrometry and the selective modification of the free thiol form of cysteine in both peptides and proteins by various quinones. This simple modification can be used to quantify the number of free or disulfide bound cysteines in a protein. In addition, quinone modification can also be used to easily probe the solvent accessibility of cysteine residues, which provides information about protein structure or folding state. Furthermore, the chromophoric properties of the quinone moiety can be leveraged for site specific photodissociation of the backbone. The photodissociation reveals both the presence and location of modified cysteine residues. For example, cleavage of the protein backbone of alpha-hemoglobin is observed selectively at a single cysteine out of 140 residues in the whole protein. This selective backbone fragmentation is accompanied by a parent ion mass loss, which is unique to the modifying quinone. When combined, this information can be used to determine both the presence and site of modification generated by naturally occurring molecules, such as dopamine, which can harness quinone chemistry to modify proteins.

Radical directed dissociation for facile identification of iodotyrosine residues using electrospray ionization mass spectrometry

Iodination of tyrosine residues in proteins has many uses in chemistry, biology, and medicine. Site specific identification of the sites of iodination is important for many of these uses. Reported herein is a facile method employing photodissociation and mass spectrometry to localize sites of iodination in whole proteins. Absorption of ultraviolet photons by iodotyrosine results in loss of iodine via homolytic bond dissociation. The resulting protein radical fragments in the vicinity of the iodotyrosine upon collisional activation. Analysis of the fragments within the vicinity of each tyrosine residue in the protein enables quantitative evaluation of the likelihood for iodination at each site. The results are compared with both traditional bottom up and top down mass spectrometric methods. Radical directed dissociation yields results in agreement with traditional approaches but requires significantly less effort and is inherently more sensitive. One limitation occurs when multiple tyrosine residues are in close proximity, in which case the extent of iodination at each residue may be difficult to determine. This limitation is frequently problematic for traditional approaches as well.

Elucidating the tertiary structure of protein ions in vacuo with site specific photoinitiated radical reactions

A new method for identifying residue specific through space contacts as a function of protein secondary and tertiary structure in the gas phase is presented. Photodissociation of a non-native carbon-iodine bond incorporated into Tyr59 of ubiquitin yields a radical site specifically at that residue. The subsequent radical migration is shown to be highly dependent on the structure of the protein. Radical-directed dissociation (RDD) of low charge states, which adopt compact structures, generates backbone fragmentation that is prominently distributed throughout the protein sequence, including residues that are distant in sequence from Tyr59. Higher charge states of ubiquitin, which adopt elongated, unfolded structures, yield RDD that is primarily nearby in sequence to Tyr59. Regardless of which structure is probed, information at the residue-level is obtained by examining specific radical-donor and radical-acceptor pairs. The relative importance of a particular interaction pair for a specific conformation can be revealed by tracking the charge state dependence of the dissociation. Structurally important contact pairs exhibit strong and concerted changes in relative intensities as a function of charge state and can also be used to reveal structural features which persist among different protein structures. Moreover, incorporation of distance constraint information into molecular mechanics conformational searches can be used to drive the search toward relevant conformational space. Implementation of this approach has revealed highly stable, previously undiscovered structures for the +4 and +6 charge states of ubiquitin, which bear little resemblance to the crystal structure.

Fragmentation of alpha-radical cations of arginine-containing peptides

Fragmentation pathways of peptide radical cations, M(+*), with well-defined initial location of the radical site were explored using collision-induced dissociation (CID) experiments. Peptide radical cations were produced by gas-phase fragmentation of Co(III)(salen)-peptide complexes [salen = N,N'-ethylenebis (salicylideneiminato)]. Subsequent hydrogen abstraction from the beta-carbon of the side-chain followed by C(alpha)-C(beta) bond cleavage results in the loss of a neutral side chain and formation of an alpha-radical cation with the radical site localized on the alpha-carbon of the backbone. Similar CID spectra dominated by radical-driven dissociation products were obtained for a number of arginine-containing alpha-radicals, suggesting that for these systems radical migration precedes fragmentation. In contrast, proton-driven fragmentation dominates CID spectra of alpha-radicals produced via the loss of the arginine side chain. Radical-driven fragmentation of large M(+*) peptide radical cations is dominated by side-chain losses, formation of even-electron a-ions and odd-electron x-ions resulting from C(alpha)-C bond cleavages, formation of odd-electron z-ions, and loss of the N-terminal residue. In contrast, charge-driven fragmentation produces even-electron y-ions and odd-electron b-ions.