Electron capture and transfer dissociation: Peptide structure analysis at different ion internal energy levels

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

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

Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass Spectrometry

Comprehensive determination of primary sequence and identification of post-translational modifications (PTMs) are key elements in protein structural analysis. Various mass spectrometry (MS) based fragmentation techniques are powerful approaches for mapping both the amino acid sequence and PTMs; one of these techniques is matrix-assisted laser desorption/ionization (MALDI), combined with in-source decay (ISD) fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR) MS. MALDI-ISD MS protein analysis involves only minimal sample preparation and does not require spectral deconvolution. The resulting MALDI-ISD MS data is complementary to electrospray ionization-based MS/MS sequencing readouts, providing knowledge on the types of fragment ions is available. In this study, we evaluate the isotopic distributions of z′ ions in protein top-down MALDI-ISD FT-ICR mass spectra and show why these distributions can deviate from theoretical profiles as a result of co-occurring and isomeric z and y-NH₃ ions. Two synthetic peptides, containing either normal or deuterated alanine residues, were used to confirm the presence and unravel the identity of isomeric z and y-NH₃ fragment ions (“twins”). Furthermore, two reducing MALDI matrices, namely 1,5-diaminonaphthalene and N-phenyl-p-phenylenediamine were applied that yield ISD mass spectra with different fragment ion distributions. This study demonstrates that the relative abundance of isomeric z and y-NH₃ ions requires consideration for accurate and confident assignments of z′ ions in MALDI-ISD FT-ICR mass spectra.

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

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

It is time for top-down venomics

The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Negative mode proteome analysis offers access to unique portions of the proteome and several acidic post-translational modifications; however, traditional collision-based fragmentation methods fail to reliably provide sequence information for peptide anions. Negative electron transfer dissociation (NETD), on the other hand, can sequence precursor anions in a high-throughput manner. Similar to other ion-ion methods, NETD is most efficient with peptides of higher charge state because of the increased electrostatic interaction between reacting molecules. Here we demonstrate that NETD performance for lower charge state precursors can be improved by altering the reagent cation. Specifically, the recombination energy of the NETD reaction-largely dictated by the ionization energy (IE) of the reagent cation-can affect the extent of fragmentation. We compare the NETD reagent cations of C₁₆H₁₀^●+ (IE = 7.9 eV) and SF₅^●+ (IE = 9.6 eV) on a set of standard peptides, concluding that SF₅^●+ yields greater sequence ion generation. Subsequent proteome-scale nLC-MS/MS experiments comparing C₁₆H₁₀^●+ and SF₅^●+ further supported this outcome: analyses using SF₅^●+ yielded 4637 peptide spectral matches (PSMs) and 2900 unique peptides, whereas C₁₆H₁₀^●+ produced 3563 PSMs and 2231 peptides. The substantive gain in identification power with SF₅^●+ was largely driven by improved identification of doubly deprotonated precursors, indicating that increased NETD recombination energy can increase product ion yield for low charge density precursors. This work demonstrates that SF₅^●+ is a viable, if not favorable, reagent cation for NETD, and provides improved fragmentation over the commonly used fluoranthene reagent. Graphical Abstract ᅟ.

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

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

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

Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins

Here we report the first implementation of activated ion electron transfer dissociation (AI-ETD) for top down protein characterization, showing that AI-ETD definitively extends the m/z range over which ETD can be effective for fragmentation of intact proteins. AI-ETD, which leverages infrared photon bombardment concurrent to the ETD reaction to mitigate nondissociative electron transfer, was performed using a novel multipurpose dissociation cell that can perform both beam-type collisional dissociation and ion-ion reactions on an ion trap-Orbitrap hybrid mass spectrometer. AI-ETD increased the number of c- and z-type product ions for all charge states over ETD alone, boosting product ion yield by nearly 4-fold for low charge density precursors. AI-ETD also outperformed HCD, generating more matching fragments for all proteins at all charge states investigated. In addition to generating more unique fragment ions, AI-ETD provided greater protein sequence coverage compared to both HCD and ETD. In all, the effectiveness of AI-ETD across the entirety of the m/z spectrum demonstrates its efficacy for robust fragmentation of intact proteins.

Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics

Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale for improved protein characterization. Furthermore, we show that activated ion electron transfer dissociation (AI-ETD), a recently introduced method for enhanced ETD fragmentation, provides useful performance with CZE separations to greatly increase protein characterization. When combined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from both standard and complex mixtures, highlighting the benefits electron-driven dissociation methods can add to CZE separations.

On the use of electron capture rate constants to describe electron capture dissociation mass spectrometry of peptides

Electron capture dissociation (ECD) tandem mass spectrometry (MS/MS) is a powerful analytical tool for peptide and protein structure analysis. The product ion abundance (PIA) distribution in ECD MS/MS is known to vary as a function of electron irradiation period. This variation complicates the development of a method of peptide identification by correlation of ECD MS/MS data with experimental and theoretical mass spectra. Here, we first develop a kinetic model to describe primary electron capture by peptide dications leading to product ion formation and secondary electron capture resulting in product ion neutralization. We apply the developed kinetic model to calculate product ion formation rate constants and electron capture rate constants of product ions from ECD mass spectra acquired using various electron irradiation periods. Contrary to ECD PIA distributions, the product ion formation rate constants are shown to be independent of electron irradiation period and, thus, may be employed to characterize ECD product ion formation more universally. The electron capture rate constants of product ions in ECD Fourier transform ion cyclotron resonance MS were found to correlate (with a correlation factor, R(2), of ca 0.9) with ion mobility cross sections of product ions in electron transfer dissociation. Finally, we demonstrate that the electron irradiation period influences the ratio of radical and even-electron c and z product ions.

Tandem mass spectrometry using the atmospheric pressure electron capture dissociation ion source

Atmospheric pressure electron capture dissociation (AP-ECD) is an emerging technique capable of being adopted to virtually any electrospray mass spectrometer, without modification of the main instrument. To date, however, because the electron capture reactions occur in the ion source, AP-ECD has been limited by its apparent inability to select precursors prior to fragmentation, i.e., to perform tandem mass spectrometry (MS/MS) experiments. In this paper we demonstrate a novel AP-ECD-MS/MS method using an AP-ECD source on a Xevo G2-S quadrupole time-of-flight (Q-TOF) mass spectrometer from Waters Micromass. The method takes advantage of the tendency for electron capture reactions to generate charge-reduced "ECnoD" products, species that have captured an electron and have had a covalent bond cleaved yet do not immediately dissociate into separate products and so retain the mass of the precursor ion. In the method, ECnoD products from the AP-ECD source are isolated in the quadrupole mass filter and induced to dissociate through supplemental activation in the collision cell, and then the liberated ECD fragment ions are mass analyzed using the high-resolution TOF. In this manner, true MS/MS spectra may be obtained with AP-ECD even though all of the precursors in the source are subjected to electron capture reactions in parallel. Here, using a late-model Q-TOF instrument otherwise incapable of performing electron-based fragmentation, we present AP-ECD-MS/MS results for a group of model peptides and show that informative, high-sequence-coverage spectra are readily attainable with the method.

On the viability of heterolytic peptide N-C(α) bond cleavage in electron capture and transfer dissociation mass spectrometry

While frequently employed as an experimental technique, the mechanistic picture surrounding the gas-phase dissociation of peptides carrying multiple positive charges during electron capture and electron transfer dissociation tandem mass spectrometry remains incomplete. Despite this mechanistic uncertainty, most proposals agree that the peptide backbone N-Cα bond located to the C-terminal (right) side of an aminoketyl radical formed in a peptide backbone during the electron capture process is homolytically cleaved. Recently, we introduced the "enol" mechanism, which proposes that a backbone N-Cα bond located to the N-terminal (left) side of an aminoketyl radical is cleaved heterolytically. Here, we further validate this mechanism using replica-exchange molecular dynamics to create unbiased representative sets of low-energy conformers for several model tryptic peptide systems (H-Alax-Lys-OH(2+), x = 3-5). Transition state barrier enthalpies for the cleavage of N-Cα bonds proceeding via the homolytic (right-side) and heterolytic (left-side) pathways, determined by density functional computations, identify the preferred cleavage route for each conformer. These findings support our original hypothesis that heterolytic N-Cα cleavage can exist in a competitive balance with homolytic cleavages, independent of the relative energy of the precursor dication species. Smaller peptide systems see decreased heterolytic N-Cα cleavage probabilities, likely resulting from an insufficient hydrogen-bonding network needed to stabilize and ultimately annihilate the transition state zwitterion. This observation may explain the early dismissal of left-side cleavage pathways based on computational studies employing small model systems.

Activated ion ETD performed in a modified collision cell on a hybrid QLT-Oribtrap mass spectrometer

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO2 laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety's high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

Identification of the structural determinants for anticancer activity of a ruthenium arene peptide conjugate

Organometallic Ru(arene)-peptide bioconjugates with potent in vitro anticancer activity are rare. We have prepared a conjugate of a Ru(arene) complex with the neuropeptide [Leu(5)]-enkephalin. [Chlorido(η(6)-p-cymene)(5-oxo-κO-2-{(4-[(N-tyrosinyl-glycinyl-glycinyl-phenylalanyl-leucinyl-NH2)propanamido]-1H-1,2,3-triazol-1-yl)methyl}-4H-pyronato-κO)ruthenium(II)] (8) shows antiproliferative activity in human ovarian carcinoma cells with an IC50 value as low as 13 μM, whereas the peptide or the Ru moiety alone are hardly cytotoxic. The conjugation strategy for linking the Ru(cym) (cym=η(6)-p-cymene) moiety to the peptide involved N-terminal modification of an alkyne-[Leu(5)]-enkephalin with a 2-(azidomethyl)-5-hydroxy-4H-pyran-4-one linker, using Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC), and subsequent metallation with the Ru(cym) moiety. The ruthenium-bioconjugate was characterized by high resolution top-down electrospray ionization mass spectrometry (ESI-MS) with regard to peptide sequence, linker modification and metallation site. Notably, complete sequence coverage was obtained and the Ru(cym) moiety was confirmed to be coordinated to the pyronato linker. The ruthenium-bioconjugate was analyzed with respect to cytotoxicity-determining constituents, and through the bioconjugate models [{2-(azidomethyl)-5-oxo-κO-4H-pyronato-κO}chloride (η(6)-p-cymene)ruthenium(II)] (5) and [chlorido(η(6)-p-cymene){5-oxo-κO-2-([(4-(phenoxymethyl)-1H-1,2,3-triazol-1-yl]methyl)-4H-pyronato-κO}ruthenium(II)] (6) the Ru(cym) fragment with a triazole-carrying pyronato ligand was identified as the minimal unit required to achieve in vitro anticancer activity.

Coordination sphere tuning of the electron transfer dissociation behavior of Cu(II)-peptide complexes

In contrast to previous electron capture dissociation (ECD) studies, we find that electron transfer dissociation (ETD) of Cu(II)-peptide complexes can generate c- and z-type product ions when the peptide has a sufficient number of strongly coordinating residues. Double-resonance experiments, ion-molecule reactions, and collision-induced dissociation (CID) prove that the c and z product ions are formed via typical radical pathways without the associated reduction of Cu(II), despite the high second ionization energy of Cu. A positive correlation between the number of Cu(II) binding groups in the peptide sequence and the extent of c and z ion formation was also observed. This trend is rationalized by considering that the recombination energy of Cu(II) can be lowered by strong binding ligands to an extent that enables electron transfer to non-Cu sites (e.g., protonation sites) to compete with Cu(II) reduction, thereby generating c/z ions in a manner similar to that observed for protonated (i.e., nonmetalated) peptides.

Combined electron transfer dissociation-collision-induced dissociation fragmentation in the mass spectrometric distinction of leucine, isoleucine, and hydroxyproline residues in Peptide natural products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(•) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm = 43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z(•) ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MS(n)) method has been successfully implemented in a liquid chromatography-MS(n) platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Repeatability and reproducibility of product ion abundances in electron capture dissociation mass spectrometry of peptides

Site-specific reproducibility and repeatability of electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) are of fundamental importance for product ion abundance (PIA)-based peptide and protein structure analysis. However, despite the growing interest in ECD PIA-based applications, these parameters have not yet been investigated in a consistent manner. Here, we first provide a detailed description of the experimental parameters for ECD-based tandem mass spectrometry performed on a hybrid linear ion trap (LTQ) FT-ICR MS. In the following, we describe the evaluation and comparison of ECD and infrared multiphoton dissociation (IRMPD) PIA methodologies upon variation of a number of experimental parameters, for example, cathode potential (electron energy), laser power, electron and photon irradiation periods and pre- irradiation delays, as well as precursor ion number. Ranges of experimental parameters that yielded an average PIA variation below 5% and 15% were determined for ECD and IRMPD, respectively. We report cleavage site-dependent ECD PIA variation below 20% and correlation coefficients between fragmentation patterns superior to 0.95 for experiments performed on three FT-ICR MS instruments. Overall, the encouraging results obtained for ECD PIA reproducibility and repeatability support the use of ECD PIA as a complementary source of information to m/z data in radical-induced dissociation applied for peptide and protein structure analysis.

Distributions of ion series in ETD and CID spectra: making a comparison

Databases which capture proteomic data for subsequent interrogation can be extremely useful for our understanding of peptide ion behaviour in the mass spectrometer, leading to novel hypotheses and mechanistic understanding of the underlying mechanisms determining peptide fragmentation behaviour. These, in turn, can be used to improve database searching algorithms for use in automated and unbiased interpretation of peptide product ion spectra. Here, we examine a previously published dataset using our established methods, in order to discover differences in the observation of product ions of different types, following ion activation and unimolecular dissociation either by collisional dissociation or the ion/ion reaction, electron transfer dissociation. Using a target-decoy database searching strategy, a large data set of precursor ions, were confidently predicted as peptide sequence matches (PSMs) at either a 1% or 5% peptide false discovery rate, as reported in our previous study. Using these high quality PSMs, we have conducted a more detailed and novel analysis of the global trends in observed product ions present/absent in these spectra, examining both CID and ETD data. We uncovered underlying trends for an increased propensity for the observation of higher members of the ion series in ETD product ion spectra in comparison to their CID counterparts. Such data-mining efforts will prove useful in the generation of new database searching algorithms which are well suited to the analysis of ETD product ion spectra.

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

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

Deamidation and transamidation of substance P by tissue transglutaminase revealed by electron-capture dissociation fourier transform mass spectrometry

Tissue transglutaminase (tTGase) catalyzes both deamidation and transamidation of peptides and proteins by using a peptidyl glutamine as primary substrate. A precise consensus sequence for the enzyme is unknown and the ratio between deamidated and transamidated (or cross-linked) reaction products is highly substrate-dependent. Due to its overlapping body distribution with tTGase and ease of manipulation with tandem mass spectrometry, we used the neuropeptide substance P as a model to investigate the associated enzymatic kinetics and reaction products. Online liquid-chromatography Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR MS) combined with electron-capture dissociation (ECD) was employed to study the tTGase-induced modifications of substance P. A particular strength of ECD for peptide-enzyme reaction product monitoring is its ability to distinguish isomeric amino acids, for example, Glu and iso-Glu, by signature product ions. Our studies show that the primary reaction observed is deamidation, with the two consecutive glutamine residues converted sequentially into glutamate: first Gln(5) , and subsequently Gln(6) . We then applied ECD FT-ICR MS to identify the transamidation site on an enzymatically cross-linked peptide, which turned out to correspond to Gln(5) . Three populations of substance-P dimers were detected that differed by the number of deamidated Gln residues. The higher reactivity of Gln(5) over Gln(6) was further confirmed by cross-linking SP with monodansylcadaverine (MDC). Overall, our approach described herein is of a general importance for mapping both enzymatically induced post-translational protein modifications and cross-linking. Finally, in vitro Ca-signaling assays revealed that the main tTGase reaction product, the singly deamidated SP (RPKPEQFFGLM-NH(2) ), has increased agonist potency towards its natural receptor, thus confirming the biologically relevant role of deamidation.

Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture

Using a modified electron transfer dissociation (ETD)-enabled quadrupole linear ion trap (QLT) mass spectrometer, we demonstrate the utility of IR activation concomitant with ETD ion-ion reactions (activated-ion ETD, AI-ETD). Analyzing 12 strong cation exchanged (SCX) fractions of a LysC digest of human cell protein extract using ETD, collision-activated dissociation (CAD), and AI-ETD, we find that AI-ETD generates 13 405 peptide spectral matches (PSMs) at a 1% false-discovery rate (1% FDR), surpassing both ETD (7 968) and CAD (10 904). We also analyze 12 SCX fractions of a tryptic digest of human cell protein extract and find that ETD produces 6 234 PSMs, AI-ETD 9 130 PSMs, and CAD 15 209 PSMs. Compared to ETD with supplemental collisional activation (ETcaD), AI-ETD generates ∼80% more PSMs for the whole cell lysate digested with trypsin and ∼50% more PSMs for the whole cell lysate digested with LysC.

Negative electron transfer dissociation of deprotonated phosphopeptide anions: choice of radical cation reagent and competition between electron and proton transfer

Despite significant developments in mass spectrometry technology in recent years, no routine proteomics sequencing tool is currently available for peptide anions. The use of a molecular open-shell cation is presented here as a possible reaction partner to induce electron transfer dissociation with deprotonated peptide anions. In this negative electron transfer dissociation (NETD) scheme, an electron is abstracted from the peptide anion and transferred to the radical cation. This is demonstrated for the example of the fluoranthene cation, C(16)H(10)(+*), which is reacted with deprotonated phosphorylated peptides in a 3-D ion trap mass spectrometer. Selective backbone cleavage at the C(alpha)-C bond is observed to yield a and x fragments, similarly to electron detachment dissociation (EDD) of peptide anions. Crucially, the phosphorylation site is left intact in the dissociation process, allowing an identification and localization of the post-translational modification (PTM) site. In contrast, NETD using Xe(+*) as the reagent cation results in sequential neutral losses (CO(2) and H(3)PO(4)) from a/x fragments, which complicate the interpretation of the mass spectra. This difference in dissociation behavior can be understood in the framework of the reduced recombination energy of the electron transfer process for fluoranthene, which is estimated at 2.5-4.5 eV, compared to 6.7-8.7 eV for xenon. Similarly to ETD, proton transfer is found to compete with electron transfer processes in NETD. Isotope fitting of the charge-reduced species shows that in the case of fluoranthene-mediated NETD, proton transfer only accounts for <20%, whereas this process highly abundant for Xe(+*) (43 and 82%). Since proton abstraction from Xe(+*) is not possible, this suggests that Xe(+*) ionizes other transient species in the ion trap, which then engage in proton transfer reactions with the peptide anions.

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.

Mapping N-terminus phosphorylation sites and quantitation by stable isotope dimethyl labeling

We have previously coupled stable isotope dimethyl labeling with IMAC enrichment for quantifying the extent of protein phosphorylation in vivo. The enhanced a(1) signal of dimethylated peptides served as a unique mass tag for unequivocal identification of the N-terminal amino acids. In this study, we demonstrate that the a(1) ion could further assist in mapping the precise phosphorylation site near the N-terminal region and allow the determination of the exact site and level of phosphorylation in one step by stable isotope dimethyl labeling. We show that the a(1) ion signal was suppressed for dimethylated peptides with a phosphorylation site at the N-terminus Ser/Thr residue (N-p*Ser/Thr) but was still enhanced for N-terminus Tyr residue (N-p*Tyr) or internal Ser/Thr residues (-p*Ser/Thr). Based on the dominant de-phosphorylated molecular ions and b-H(3)PO(4) ions for N-p*Ser/Thr, we propose that dimethyl labeling increases the basicity of the N-terminus and accelerates the de-phosphorylation for N-p*Ser/Thr precursors, which, however, suppresses the a(1) ion enhancement due to the resulting unsaturated covalent bond on C(alpha) of the N-terminus amino acid. Using this method, we excluded three Ser/Thr phosphorylation sites in A431 cells, two of which, however, were previously reported to be phosphorylation sites; we confirmed three known phosphorylation sites in A431 cells and quantified their ratios upon EGF treatment. Notably, we identified a novel phosphorylation site on Ser43 residue at N-terminus of the tryptic peptide derived from SVH protein in pregnant rat uteri. SVH protein has not been reported or implied with any phosphorylation event, and our data show that the Ser43 of SVH is an intrinsic phosphorylation site in pregnant rat uteri and that its phosphorylation level was slightly decreased upon c-AMP treatment.

Electron capture dissociation mass spectrometry of tyrosine nitrated peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.

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

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

Enhanced electron transfer dissociation through fixed charge derivatization of cysteines

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

Electron capture dissociation product ion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate with amino acid polarity and radical stability

We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity. The results obtained on a series of model H-RAAAAXAAAAK-OH peptides confirm a direct correlation of ECD PIA with X amino acid hydrophobicity and polarity. The correlation factor (R) exceeds 0.9 for 12 amino acids (Ile, Val, His, Asn, Asp, Glu, Gln, Ser, Thr, Gly, Cys, and Ala). The deviation of ECD PIA for seven outliers (Pro is not taken into consideration) is explained by their specific radical stabilization properties (Phe, Trp, Tyr, Met, and Leu) and amino acid basicity (Lys, Arg). Phosphorylation of Ser, Thr, and Tyr decreases the efficiency of ECD around phosphorylated residues, as expected. The systematic arrangement of amino acids reported here indicates a possible route toward development of a predictive model for quantitative electron capture/transfer dissociation tandem mass spectrometry, with possible applications in proteomics.

Data-dependent electron transfer dissociation of large peptides and medium size proteins in a QTOF instrument on a liquid chromatography timescale

Liquid chromatography (LC) electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) of protein digests is demonstrated in a hybrid quadrupole-hexapole orthogonal time-of-flight (OTOF) mass spectrometer. Analyte ions are selected in a mass-analyzing quadrupole, accumulated in the hexapole linear ETD reaction cell and mutually stored with ETD reagent anions. Product ions are collected in an ion cooler and then analyzed by an OTOF mass analyzer. The hexapole structure of the ETD reaction cell allows for a broad fragment ion mass range distribution and a high ion storage capacity. Analytically useful ETD OTOF-MS/MS spectra could be obtained at a rate of faster than 2 Hz. When used in conjunction with LC this high speed allows for several MS and MS/MS spectra to be obtained across each LC peak. An MS scan is used to select the precursor ions. With a 1 m flight tube and single reflection, resolutions of about 10 k and a mass accuracy of 5 ppm were achieved. When analyzing a 100 fmol solution of a tryptic digest of bovine serum albumin (BSA) by LC/ETD MS/MS, 27 unique peptides were identified with a summed Mascot score of 1316 using the Swiss Prot database. In addition, we explored the capability for analyzing small proteins with the present hybrid instrument. ETD MS/MS of intact ubiquitin ([M+12H](12+)) leads to the identification of the protein with a Mascot score of 264.

Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, contrary to preferential channels of fragmentation in slow heating-based tandem mass spectrometry. Here we demonstrate that for amphipathic peptides and proteins, modulation of ECD product ion abundance (PIA) along the sequence is pronounced. Moreover, because of the specific primary (and presumably secondary) structure of amphipathic peptides, PIA in ECD demonstrates a clear and reproducible periodic sequence distribution. On the one hand, the period of ECD PIA corresponds to periodic distribution of spatially separated hydrophobic and hydrophilic domains within the peptide primary sequence. On the other hand, the same period correlates with secondary structure units, such as alpha-helical turns, known for solution-phase structure. Based on a number of examples, we formulate a set of characteristic features for ECD of amphipathic peptides and proteins: (1) periodic distribution of PIA is observed and is reproducible in a wide range of ECD parameters and on different experimental platforms; (2) local maxima of PIA are not necessarily located near the charged site; (3) ion activation before ECD not only extends product ion sequence coverage but also preserves ion yield modulation; (4) the most efficient cleavage (e.g. global maximum of ECD PIA distribution) can be remote from the charged site; (5) the number and location of PIA maxima correlate with amino acid hydrophobicity maxima generally to within a single amino acid displacement; and (6) preferential cleavage sites follow a selected hydrogen spine in an alpha-helical peptide segment. Presently proposed novel insights into ECD behavior are important for advancing understanding of the ECD mechanism, particularly the role of peptide sequence on PIA. An improved ECD model could facilitate protein sequencing and improve identification of unknown proteins in proteomics technologies. In structural biology, the periodic/preferential product ion yield in ECD of alpha-helical structures potentially opens the way toward de novo site-specific secondary structure determination of peptides and proteins in the gas phase and its correlation with solution-phase structure.