Abundant b-type ions produced in electron capture dissociation of peptides without basic amino acid residues

Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins

Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND₃, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N₂-gas over a deuterated ND₃/D₂O solution, or by leading purified ND₃-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.

General rules of fragmentation evidencing lasso structures in CID and ETD

Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring.

Analysis of argentinated peptide complexes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Peptide = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, neurotensin

RATIONALE

The increased use of silver nanoparticles (AgNPs) for various biological applications, and over-expression of various peptide receptors in different tumors/cancer cells, necessitate the need for dedicated investigations on the intrinsic binding ability of Ag with various biologically important peptides for better understanding of AgNPs-peptide interactions and for the future development of contrasting agents as well as drugs for imaging/biomedical applications.

METHODS

The [M+(Ag)n ](+) complexes are prepared and characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS).

RESULTS

Silver complexes of the peptides [M+(Ag)n ](+) , where M = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, have been investigated for their intrinsic Ag(+) -binding ability. Unusual binding of up to seven Ag(+) with these small peptides is observed. The mass spectra show n = 1-5 for bombesin and somatostatin, n = 1-6 for bradykinin and arg(8) -vasopressin, and n = 1-7 for oxytocin and neurotensin. In addition, oxytocin and arg(8) -vasopressin show the formation of dimers and their complexes [M2 +(Ag)n ](+) with n = 1-8 and n = 1-5, respectively. The possible amino acid residues responsible for Ag(+) binding in each peptide have been identified on the basis of density functional theory (DFT)-calculated binding energy values of Ag(+) towards individual amino acids.

CONCLUSIONS

Mass spectrometric evidence indicates that the peptides, viz., oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, show greater affinity for Ag(+) . Hence, they may be used as carriers for AgNPs in targeted drug delivery as well as an alternative for iodinated contrasting agents in dual energy X-ray imaging techniques. Radio-labeled Ag with these peptides can also be used in radio-pharmaceuticals for diagnostic and therapeutic applications. Copyright © 2016 John Wiley & Sons, Ltd.

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.

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.

Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry

Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.

Topoisomer differentiation of molecular knots by FTICR MS: lessons from class II lasso peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminal macrolactam ring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collision-induced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECD spectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c•/z from c/z•) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions (b'/•(n)). We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z• and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture.

Peptide fragmentation by corona discharge induced electrochemical ionization

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M](+·), thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides, and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: (1) complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; (2) electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e(-) → Fe(+·)); (3) radical fragmentation of the complexed compound; (4) electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites.

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.

Prediction of electron-transfer/capture dissociation spectra of peptides

An empirical model, based on classic kinetics, was developed for quantitative prediction of electron-transfer dissociation (ETD) and electron-capture dissociation (ECD) spectra of peptides. The model includes most fragmentation pathways described in the literature plus some additional pathways based on the author's assumptions and observations. The ETD model was trained with more than 7000 ETD spectra, with and without supplemental activation. The ECD model was trained with more than 6000 ECD spectra. The trained ETD and ECD models are able to predict ETD and ECD spectra with reasonable accuracy in ion intensities for peptide precursors up to 4000 u in mass.

Charge remote fragmentation in electron capture and electron transfer dissociation

Secondary fragmentations of three synthetic peptides (human alphaA crystallin peptide 1-11, the deamidated form of human betaB2 crystallin peptide 4-14, and amyloid beta peptide 25-35) were studied in both electron capture dissociation (ECD) and electron-transfer dissociation (ETD) mode. In ECD, in addition to c and z. ion formations, charge remote fragmentations (CRF) of z. ions were abundant, resulting in internal fragment formation or partial/entire side-chain losses from amino acids, sometimes several residues away from the backbone cleavage site, and to some extent multiple side-chain losses. The internal fragments were observed in peptides with basic residues located in the middle of the sequences, which was different from most tryptic peptides with basic residues located at the C-terminus. These secondary cleavages were initiated by hydrogen abstraction at the alpha-, beta-, or gamma-position of the amino acid side chain. In comparison, ETD generates fewer CRF fragments than ECD. This secondary cleavage study will facilitate ECD/ETD spectra interpretation, and help de novo sequencing and database searching.

Electron capture dissociation of peptide hormone changes upon opening of the tocin ring and complexation with transition metal cations

Electron capture dissociation (ECD) is an analytical technique in mass spectrometry (MS) that allows detailed structural study of biomolecules to gain insight in their function. In this work the ECD behavior of two peptide hormones oxytocin (OT1) and vasopressin (VP1) was studied. The results of OT1 and VP1 were compared to structural analogues OT2 and VP2, which have similar amino acid sequences but lack the tocin ring. The ECD results showed that both the fragment type (c/z versus b/y) and the cleavage sites (ring versus tail) changed upon opening of the tocin ring. All four peptides were complexed with three different transition metal cations (Zn(2+), Ni(2+) and Cu(2+)) and the ECD results were compared to those obtained from the doubly protonated species. The use of various metal ions yielded different cleavages sites within the same peptide. This can be an effect of the metal ion itself, or a consequence of a change in conformation as was suggested earlier. In addition, the type of fragment ion varied for each metal-complexed peptide, which is in agreement with previous observations.

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.