Top-Down Charge Transfer Dissociation (CTD) of Gas-Phase Insulin: Evidence of a One-Step, Two-Electron Oxidation Mechanism
Top-down analyses of protonated insulin cations of charge states of 4+, 5+, or 6+ were performed by exposing the isolated precursor ions to a beam of helium cations with kinetic energy of more than 6 keV, in a technique termed charge transfer dissociation (CTD). The ~100 ms charge transfer reaction resulted in approximately 20% conversion efficiency to other intact charge exchange products (CTnoD), and a range of low abundance fragment ions. To increase backbone and sulfide cleavages, and to provide better structural information than straightforward MS2 CTD, the CTnoD oxidized products were isolated and subjected to collisional activation at the MS3 level. The MS3 CTD/CID reaction effectively broke the disulfide linkages, separated the two chains, and yielded more structurally informative fragment ions within the inter-chain cyclic region. CTD also provided doubly oxidized intact product ions at the MS2 level, and resonance ejection of the singly oxidized product ion revealed that the doubly oxidized product originates directly from the isolated precursor ion and not from consecutive CTD reactions of a singly oxidized intermediate. MS4 experiments were employed to help identify potential radical cations and diradical cations, but the results were negative or inconclusive. Nonetheless, the two-electron oxidation process is a demonstration of the very large potential energy (>20 eV) available through CTD, and is a notable capability for a 3D ion trap platform.
KeywordsTop-down analysis Intact protein Novel fragmentation Radical cation Peptide sequencing Ion chemistry
B-cells in Langerhans of the pancreas produces insulin, which not only maintains the blood glucose levels from getting too high or too low, but also regulates the amino acid uptake and inhibits the breakdown of glycogen, protein, and fat . Analogous to many polypeptide species, insulin contains multiple disulfide linkages for stabilizing its three-dimensional structure, and these disulfide bonds ensure the correct biological function. The multiple disulfide linkages form intra-chain and inter-chain cyclic structures, the presence of which inhibits the structural analysis of insulin via tandem mass spectrometry approaches. To retrieve the primary sequence information within the inter-chain cyclic regions, certain techniques have been employed to disrupt disulfide linkages.
Mass spectrometry (MS) shows high selectivity and sensitivity, and the capability of performing a variety of experiments, which makes it an appealing technique for analyzing biological molecules . Owing to the advent of soft ionization methods such as electrospray ionization (ESI)  or matrix-assisted laser desorption ionization (MALDI) , biomolecular ions can be formed intact for the purposes of molecular weight determination. The development of tandem mass spectrometry (MS/MS or MS2) has greatly advanced the application of MS to the structural characterization of biomolecules .
Disulfide linkage-containing polypeptides have been extensively examined during the past few decades using various MS/MS techniques, including collision-induced dissociation (CID) [6, 7, 8, 9], post-source decay (PSD) , electron capture dissociation (ECD) [10, 11, 12], electron transfer dissociation (ETD) [9, 13, 14, 15, 16, 17], electron-induced dissociation (EID) , electron detachment dissociation (EDD) , infrared multiphoton dissociation (IRMPD) , and ultraviolet photodissociation (UVPD) [20, 21, 22, 23, 24]. As the most widely used ion activation technique , CID makes use of ion/molecule collisions to convert kinetic energy to internal energy for the purpose of fragmenting the target ion. For peptides, CID mainly gives rise to b and y fragment ions from backbone amide bond cleavages. Insulin, at various charge states of 1+, 2+, 3+, 4+ and 5+ has been investigated with CID, and the fragmentation efficiency is strongly dependent on the precursor charge state . One particular limitation of CID is that little or limited sequence information is retreived within the cyclic regions . Electron-based ion activation methods, like ECD, has shown the capability to cleave disulfide bonds, but ECD exhibited a relatively low dissociation efficiency . Julian and coworkers combined UV activation with ECD to fragment insulin, which broke all three-disulfide bonds of insulin and exhibited a more extensive backbone fragmentation than ECD alone . In other work, Loo and coworkers employed sulfolane as the supercharging reagent in protein solution, and the resulting supercharged protein ions exhibited elevated ECD efficiency and S–S bond dissociation efficiency .
Charge transfer dissociation (CTD) using helium is an alternative MS/MS technique was developed by the Jackson research group  and is very similar in energy and mechanism to metastable atom-activated dissociation (MAD) [29, 30, 31, 32, 33, 34, 35]. CTD employs helium cations with kiloelectronvolt kinetic energies to bombard the target peptide cations, which can produce a nearly complete set of a ions from 1+ substance P . CTD also promotes radical ion fragmentation of peptides and oligosaccharides [36, 37, 38, 39]. In the present work, we explore the possibility of integrating CTD into a top-down workflow for small proteins by fragmenting the 4+, 5+, and 6+ charge states of bovine insulin with CTD. Whereas the resulting fragmentation pattern is very similar to ETD fragmentation demonstrated by others, we demonstrate the occurrence of an unexpected one-step, two-electron oxidation pathway, which highlights the unprecedented high energy that is available through CTD. We also characterize the difference between radical fragmentation pathways and even-electron pathways for hydrogen-deficient and hydrogen-rich radical cations.
All experiments were performed on a modified Bruker instrument (Bruker Daltonics, Bremen, Germany) equipped with a saddle field fast ion gun installed on the top of ring electrode [28, 30]. Briefly, a 2-mm hole was drilled in the ring electrode for the permission of helium cations into the trap. The saddle field fast ion source was used as the helium cation source. The ion source was installed onto a three-dimensional quadrupole ion trap (QIT) mass spectrometer. The instrument modification is described in detail elsewhere .
Bovine insulin was purchased from Sigma-Aldrich (St. Louis, MO, USA) and used without further purification. The insulin solution was prepared with a final concentration of approximately 20 μM in 49.5/49.5/1 (v/v/v) methanol/water/glacial acetic acid. Methanol (HPLC-grade) and glacial acetic acid were purchased from Fisher Scientific (Waltham, MA, USA). Water was obtained from an in-house Milli-Q purification system with >18 MΩ salt content.
Mass Spectrometry Measurement
All mass spectra were collected in positive mode with an ESI voltage of 4.5 kV, capillary voltage of 8 V, capillary temperature of 250 °C, and a heated ESI source temperature of 60 °C. The helium trap pressure, as measured in the main vacuum chamber, was 1.2 × 10–5 mbar. Full mass spectra were collected at different operating m/z ranges depending on the precursor ion. Fragment ions were assigned if they are within ±0.8 mass unit of the corresponding theoretical value, and if they were accompanied by at least one isotope peak to confirm the charge state via the expected isotope peak spacing.
Collision-Induced Dissociation Measurements
The precursor ion of interest was isolated using a selection window of ±4 Da relative to the selected centroid m/z value. The ion current control (ICC) module was deactivated and the accumulation time (injection time) was typically 1.0 ms. The low mass cutoff (LMCO) was typically set to be approximately ~¼ of the precursor mass; e.g., for 5+ insulin (m/z 1148.0), the LMCO was set to be m/z 300. The CID amplitude was set to be ~0.30 V and “SmartFrag” mode was disabled. A typical CID experiment used 1.5 min of averaged spectra.
Charge Transfer Dissociation Measurements
CTD experiments were conducted similarly to CID experiments, except that the QIT injection time was set to be 50 ms. A variable leak-valve was used to control the flow of the helium (1.20 × 10–5 mbar) through the ion gun. CTD was performed by the introduction of helium cations into the three-dimensional quadrupole ion trap. A waveform generator was synchronized with the period reserved for CID fragmentation. The waveform generator was triggered by a TTL signal from the mass spectrometer, the details of which are provided elsewhere . A typical CTD experiment consists of a 2.5 min period of CTD product ion accumulation spectra and a 2.0 min period of background accumulation spectra (i.e., helium beam on but ESI off). The time-averaged background spectrum was subtracted from the time-averaged product ion spectrum. In the MS3 CID experiments, CTD-generated product ions were isolated and subjected to a CID amplitude of 0.25 V at the MS3 level. The follow-up isolation/ion storage experiments (MS4 level) were carried out using a similar procedure. At the MS4 stage, the isolation window was 10 Da and the LMCO was 500.
Resonance ejection experiments were conducted for the investigation of dissociation pathways. The precursor ions of interest were isolated and subjected to helium irradiation at the MS2 level. A particular product ion could then be resonantly ejected during the CTD reaction through the application of a relatively large CID amplitude (~2.5 V) at a frequency that corresponded to the desired intermediate. The experiment was repeated three times, and all the product ion spectra were averaged for final analysis. The experiment was repeated with the CID amplitude set to 0 V to ensure that the factor of scattering losses due to prolonged storage was independent of the factor of resonance ejection.
Results and Discussion
The presence of charge-reduced product ions, for example [M + 4H]3+•, indicates that a side channel of ETD-like behavior is occurring. We recently described an attempt to characterize the potential reagent anions , which showed that the reagent anions originate from background contamination, are radical anions, and are highly unsaturated. The reagent negative ions appear to comprise a homologous series, which maximizes in abundance around m/z 184–220. The CTD activation of large mass precursor-like insulin permitted the LMCO to be raised to m/z 300 to prevent the co-accumulation of the background reagent anions and thereby reduce the extent of the competing ETD reaction. The benefit of operating with an elevated LMCO is that the ETD pathway is minimized and the oxidized products of insulin are generally more abundant than the charge-reduced product ions, as shown in Figure 1a.
Explicit radicals are not labeled on fragment ions (i.e., z ions) because the 3D ion trap does not have the mass accuracy or resolving power to make confident assignments about the exact masses of the different fragment ions. Many fragments, such as z ions and a + 1 ions, are most likely radical .
Compared with the results from 4+ and 5+ insulin, CTD of 6+ insulin produced many more fragment ions, as shown in Figure 3. In contrast to CID , ETD  and ECD  CTD of 6+ insulin produced a set of contiguous z ions; i.e., Bz 4, Bz 5, and Bz 6 (in red font). Similar to the CTD results of 5+ insulin, these fragments arise from the cleavage of C-terminus of chain B and outside the inter-chain cyclic region. One fragmentation product of chain A was observed (Aa 4), which originates from the cleavage of the N-terminus of chain A: again, outside the cyclic region.
A set of doubly charged contiguous y ions from chain B; i.e., By 10 2+, By 11 2+, By 12 2+, By 13 2+, and By 14 2+ (blue font), was also observed from the 6+ precursor, which are rarely observed in other MS/MS experiments. Fragmentation in these region appears rather unique to CTD, since most techniques (CID [7, 8], ETD , ECD/AI ECD ) struggle to induce fragmentation in this region. The By 10 2+ and By 11 2+ fragments are formed from the cleavage of C-terminus of chain B, outside the inter-chain cyclic region, but the formation of By 12 2+, By 13 2+, and By 14 2+ requires breakage of both inter-chain disulfide linkages in addition to the backbone cleavage. Similarly, the ions Ba 10, Ba 11 2+, and Ba 12 also require the cleavage of both disulfide linkages. Additionally, this set of internal-fragment ions also distinguishes CTD from the other techniques, despite the otherwise remarkable similarity between CTD and ETD  for exocyclic cleavages. All the above observations indicate that CTD can directly cleave backbone and disulfide linkages in a single activation step, and is thereby capable of providing some primary sequence information within the cyclic regions.
The above CTD results have also shown a dependence of CTD behavior on the charge state of the precursor ions. The dependence of CTD behavior upon low precursor charge states (1+, 2+, and 3+) of smaller peptides has been studied in our previous work . In this study, as the precursor charge state increased from 4+ to 6+, an increase in the number of fragment ions was observed. This means more bonds and a greater variety of bonds were cleaved at higher precursor charge states, which is consistent with previous studies using ETD . However, unlike ETD, CTD is not expected to become more efficient or more exothermic as the charge state of the precursor increases. In fact, one would expect the efficiency and efficacy of cation–cation reactions in CTD to decrease as the charge sate of the precursor ion increases. It therefore seems possible that the improvement in product ions observed through CTD of the 6+ precursor could in fact be due to unwanted ETD side reactions. Another possibility is that the increase in charge state of the 6+ precursor enhances the extent of protein unfolding, thus making the protein more susceptible to fragmentation when interacting with helium cations.
The backbone cleavages preferentially occur near the C-terminus of chain B—which is consistent with the ECD and ETD work of others [8, 10, 14, 24]—and in regions close to aromatic residues, like tyrosine, which also has been noted by others . Compared with ETD, CTD does not produce as many fragment ions near the N-terminus of chain B for 6+ insulin precursor. ETD excels in retrieving primary sequence information outside the cyclic regions, but only occasionally provides backbone information within the cyclic regions [14, 26]. In CID experiments of 5+ insulin [6, 8], all the cleavages occurred in regions external to the disulfide bonds and no structurally informative fragments were obtained from within the cyclic regions. To increase the sequence coverage and probe the fragmentation mechanism, we therefore used supplemental collisional activation to fragment the primary product ions that underwent oxidation without dissociation; i.e., the CTnoD product ions.
To examine the congested area in Figure 5, a narrow region of the spectrum (m/z 1110–1180) is expanded in Supplementary Figure S4. Analogous to MS3 CTD/CID experiment of [insulin + 6H]7+•, a complementary chain adduct ion pair—[Chain A]2+ and [Chain B]3+—was also observed for [insulin + 4H]5+•. It is noteworthy that intact Chain A is always formed in the 2+ charge state, regardless of the precursor charge sate undergoing CTD. Moreover, the sum of the charge states of the two individual chain adduct ions equals that of the precursor insulin adduct ion. The distribution of product ion charge states agrees closely with the results from CID reaction of gold-cationized insulin . In the gold-adducted insulin studies, McLuckey and coworkers also observed complementary chain adduct pairs ([B-chain]4+/[A-chain]1+ and [B-chain]3+/[A-chain]2+) in their MS3 ETD/CID experiment of [insulin+5H]5+/[insulin+6H]5+• . They reasoned that the radical nature of [M + 6H]5+• could account for the insulin chain separation in this MS3 experiments . The analogous charge-state split of precursor ions—asymmetric pattern—has also been widely reported in low-energy CID experiments of other protein complex ions [39, 40].
To determine whether the individual chain adduct ions ([Chain A]2+ and [Chain B]3+) are radical species or even-electron species, each of them was isolated at MS4-level and stored in the ion trap for 200 ms to react with background oxygen (Supplementary Figures S5 and S6). It has been reported that when the radical z-ions of peptides are stored in the electrodynamic ion trap at room temperature, they often react with residual oxygen. The addition of O or O2 to distonic radical cations has been observed in ETD , fs-LID , He-MAD , and He-CTD . However, oxygen-attachment was not observed for either [Chain A]2+ or [Chain B]3+, indicating that the two types of individual chain adduct ions are more likely to be even-electron species, or that the radical resides on the sulfur atoms and does not undergo the typical oxygen addition of z ions. The theoretical mass to charge ratio of monoisotopic [Chain A + 2H]2+ is 1169.995. This theoretical mass contrasts with the lightest of the measured isotope cluster of the A2+ ions, which appears at m/z 1168.0 in Figure 4b. The A2+ ion must therefore be hydrogen deficient by two hydrogens (2H• or H2). The 2 Da loss mechanism from chain A is not known at this time.
The fragmentation behavior of the individual chain adduct ions has been well-documented in literature. For example, Zubarev and coworkers observed doubly charged peptide monomers attributable to the cleavage of an S–S bond in UVPD experiments . In similar work, Wongkongkathep et al.  showed that ESI-generated 6+ insulin could be mass-selected and irradiated by 266 nm UV laser to provide the individual Chain A/B fragments. McLafferty and coworkers have reported singly charged peptide monomers corresponding to the breakage of a S–S bond in ECD experiments .
Different from ETD/ECD, which are dominated by charge-reduction and hydrogen rich radical cations, CTD is dominated by charge increased and hydrogen-deficient radical cations, with a smaller contribution of charge-decreased products . Given the previous discussions on the charge-increased product [insulin + 4H]5+•, MS3 CID spectrum of the charge-decreased product [insulin + 6H]5+• derived from CTD of [insulin + 6H]6+ was collected as well (Supplementary Figure S7). Analogous to MS3 CID experiment for charge-increased species ([insulin + 4H]5+•), complementary chain adduct ion pair—[Chain A]2+ and [Chain B]3+—was also observed from CID of the charge-reduced species ([insulin + 6H]5+•). This observation is consistent with the work of McLuckey and coworkers’ publication , which involved ETD as the source for generating of [insulin + 6H]5+•. The consistency indicates a robust similarity between the radical intermediates that seems independent of a hydrogen transfer mechanism.
The CTD-generated [insulin + 5H]6+• was also isolated and subjected to collisional activation. The resulting MS3 CID spectrum (Supplementary Figure S3) provided greater fragmentation efficiency and better signal-to-noise (S/N) ratio than [insulin + 4H]5+•. CID of [insulin + 5H]6+• produced more y ions outside the cyclic regions on the C-terminus of chain B. Consistent with the above CID results of the CTnoD products, CID of [insulin + 5H]6+• also produced individual chain adduct ion pair: [Chain A]2+ and [Chain B]4+.
Figure 6a shows a regular CTD spectrum of the [M + 5H]5+, in which both [M + 5H] 6+• and [M + 5H]7+•• were present. In Figure 6b, the first-generation product ion, and possible intermediate, [M + 5H]6+• was resonantly ejected during CTD. Figure 6b clearly shows that even in the presence of simultaneous ejection of [M + 5H]6+•, the product ion [M + 5H]7+•• is still readily observable. Quantitation of the peak heights using three sets of alternating spectra of CTD with and without resonance ejection (Supplementary Figure S6) showed no significant decrease in the product ion abundance with the resonance ejection in place. These results clearly demonstrate that the formation of [M + 5H]7+•• is not affected by the immediate removal of [M + 5H]6+• and that the product ion [M + 5H]7+•• is therefore a direct product of the two-electron oxidation pathway provided pathway A (Equation 4).
Consistent with the previous result, when [M + 6H]7+• was resonantly ejected during CTD of [M + 6H]6+, the intensity of two-electron oxidation product [M + 6H]8+•• was also unaffected by the removal of the potential intermediate (Supplementary Figure S8). These resonance ejection experiments verify that the doubly ionized ion is formed directly from the protonated precursor ion via a one-step two-electron process. The peak intensities in Figure 6 and Supplementary Figure S8 are statistically verified in the Supporting Information (Supplementary Tables S1 and S2, and Supplementary Figure S9).
The ability to perform a one-step removal of two electrons (double ionization) has been reported once before by Zubarev and coworkers in their electron ionization dissociation (EID) experiments  in an FT-ICR platform. Zubarev et al. were able to produce doubly ionized species, [M + nH](n+2)+, by bombarding peptide cations ([M + nH] n+, n ≥ 1) with ≥40 eV electrons. However, these species from 1+ and 2+ precursors were more difficult to discern in the FT-ICR than ≥3+ precursors because of their overlap with the third and second parasitic harmonics of the precursors. To our knowledge, such high-energy activation (≥20 eV) barriers have only been reported in the high-energy EID experiments on an FT-ICR platform, which makes it all the more unusual to replicate the capability on a low-cost QIT mass spectrometer.
To further probe the behavior of the doubly ionized species, two follow-up experiments were conducted. First, [insulin + 5H]7+•• (or [insulin + 6H]8+••) generated from CTD of [insulin + 5H]5+ (or [insulin + 6H]6+) was isolated at the MS3 level and confined in the ion trap for an extra 200 ms to see if the oxidized products would react with residual oxygen in a manner that distonic radical cations are prone to do. The isolation spectra are shown in Supplementary Figures S10a and S11a, respectively, and indicate the successful mass-selection at MS3 level. However, with the addition of a 200 ms reaction of [insulin + 5H]7+•• or [insulin + 6H]8+•• with residual oxygen, neither charge state resulted in any oxygen attachment. The absence of oxygen attachment does not exclude the possibility of diradical [insulin + 5H]7+•• and [insulin + 6H]8+•• because their structure/configuration might simply prevent them from reacting with residual oxygen in the ion trap.
Secondly, [insulin+5H]7+•• was mass-selected in the same way as shown in Supplementary Figure S10a. Instead of ion storage, [insulin+5H]7+•• was fragmented with a CID amplitude of 0.3 V at MS3 level (Supplementary Figure S12). Seven fragment ions were observed, most of which originate from the cleavage of B-chain. Only one fragment ion originates from the cleavage of A-chain. For comparison purposes, the CID spectrum of ESI-generated [insulin + 7H]7+ was collected as well (Supplementary Figure S13). Thirteen B-chain fragment ions were observed, among which a contiguous ion set (By 3, By 4, By 5) was generated. Similar to the MS3 CTD/CID spectrum, only one A-chain fragment ion was observed. The fragment map comparison of the above experiments is shown in Supplementary Scheme S1. Unfortunately, the signal to noise ratio for MS3 CID of the doubly ionized species ([insulin + 5H]7+••) was too poor to determine whether or not the fragmentation pattern is significantly different than that of [insulin + 6H]7+•. Although the ability to perform a one-step two-electron oxidation reaction in the gas phase does not appear to be beneficial for the analysis of insulin or disulfide-linked peptides, there will no doubt be other applications that could benefit from such a capability.
ESI-generated insulin cations (at charge states of 4+, 5+, and 6+) were subjected to helium-cation irradiation, producing both charge-increased species and charge-decreased species. These species are accompanied by a few fragment ions, the number and relative abundances of which are highly dependent on the precursor charge state;6+ Insulin produced the maximum number of fragment ions, most of which originate from the cleavages of B-chain outside the cyclic regions defined by the disulfide linkages. The charge-increased product ions from the CTD process were further mass-selected and subjected to CID reaction at the MS3 level. This approach effectively broke disulfide linkages, showing the capability of producing more fragment ions than a single CTD experiment. Resonance ejection experiments were conducted during CTD experiments to prevent consecutive CTD reactions. Instead of the commonly observed one-electron oxidation pathways, an interesting one-step two-electron oxidation pathway for the formation of [M + nH](n+2)+•• was revealed, which has an activation barrier of at least 20 eV. The diradical nature of the doubly oxidized product could not be confirmed through reaction with residual oxygen or by CID. The above results, along with the low-cost instrument platform, indicate that CTD is an intriguing high-energy fragmentation method for the structural interrogation of gas-phase biomolecules.
The authors acknowledge financial support from the National Institutes of Health (NIH) (1R01GM114494-01). The opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of NIH.
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