Collisional activation of peptide ions in FT-ICR mass spectrometry

Quantum versus classical unimolecular fragmentation rate constants and activation energies at finite temperature from direct dynamics simulations

In the present work, we investigate how nuclear quantum effects modify the temperature dependent rate constants and, consequently, the activation energies in unimolecular reactions. In the reactions under study, nuclear quantum effects mainly stem from the presence of a large zero point energy. Thus, we investigate the behavior of methods compatible with direct dynamics simulations, the quantum thermal bath (QTB) and ring polymer molecular dynamics (RPMD). To this end, we first compare them with quantum reaction theory for a model Morse potential before extending this comparison to molecular models. Our results show that, in particular in the temperature range comparable with or lower than the zero point energy of the system, the RPMD method is able to correctly capture nuclear quantum effects on rate constants and activation energies. On the other hand, although the QTB provides a good description of equilibrium properties including zero-point energy effects, it largely overestimates the rate constants. The origin of the different behaviours is in the different distance distributions provided by the two methods and in particular how they differently describe the tails of such distributions. The comparison with transition state theory shows that RPMD can be used to study fragmentation of complex systems for which it may be difficult to determine the multiple reaction pathways and associated transition states.

FT-MS in the de novo top-down sequencing of natural nontryptic peptides

The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.

TUTORIAL: ION ACTIVATION IN TANDEM MASS SPECTROMETRY USING ULTRA-HIGH RESOLUTION INSTRUMENTATION

Tandem mass spectrometry involves isolation of specific precursor ions and their subsequent excitation through collision-, photon-, or electron-mediated activation techniques in order to induce unimolecular dissociation leading to formation of fragment ions. These powerful ion activation techniques, typically used in between mass selection and mass analysis steps for structural elucidation, have not only found a wide variety of analytical applications in chemistry and biology, but they have also been used to study the fundamental properties of ions in the gas phase. In this tutorial paper, a brief overview is presented of the theories that have been used to describe the activation of ions and their subsequent unimolecular dissociation. Acronyms of the presented techniques include CID, PQD, HCD, SORI, SID, BIRD, IRMPD, UVPD, EPD, ECD, EDD, ETD, and EID. The fundamental principles of these techniques are discussed in the context of their implementation on ultra-high resolution tandem mass spectrometers. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide

Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).

Introduction to Mass Spectrometry-Based Proteomics

Mass spectrometry, a technology to determine the mass of ionized molecules and biomolecules, is increasingly applied for the global identification and quantification of proteins. Proteomics applies mass spectrometry in many applications, and each application requires consideration of analytical choices, instrumental limitations and data processing steps. These depend on the aim of the study and means of conducting it. Choosing the right combination of sample preparation, MS instrumentation, and data processing allows exploration of different aspects of the proteome. This chapter gives an outline for some of these commonly used setups and some of the key concepts, many of which later chapters discuss in greater depth. Understanding and handling mass spectrometry data is a multifaceted task that requires many user decisions to obtain the most comprehensive information from an MS experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools addresses the many analytical challenges. This chapter revises the basic concept in mass spectrometry (MS)-based proteomics.

Statistical molecular fragmentation: which parameters influence the branching ratios?

Our recently developed statistical model for molecular fragmentation (SMF) is used to study the decomposition of propane and to predict thermodynamically controlled yields of products as a function of excitation energy deposited into propane.

Investigation of Hemicryptophane Host-Guest Binding Energies Using High-Pressure Collision-Induced Dissociation in Combination with RRKM Modeling

In advancing host-guest (H-G) chemistry, considerable effort has been spent to synthesize host molecules with specific and well-defined molecular recognition characteristics including selectivity and adjustable affinity. An important step in the process is the characterization of binding strengths of the H-G complexes that is typically performed in solution using NMR or fluorescence. Here, we present a mass spectrometry-based multimodal approach to obtain critical energies of dissociation for two hemicryptophane cages with three biologically relevant guest molecules. A combination of blackbody infrared radiative dissociation (BIRD) and high-pressure collision-induced dissociation (high-pressure CID), along with RRKM modeling, was employed for this purpose. For the two tested hemicryptophane hosts, the cage containing naphthyl linkages exhibited stronger interactions than the cage bearing phenyl linkages. For both cages, the order of guest stability is choline > acetylcholine > betaine. The information obtained by these types of mass spectrometric studies can provide new insight into the structural features that most influence the stability of H-G pairs, thereby providing guidance for future syntheses. Graphical Abstract.

Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis

Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.

Structures and Superhalogen Properties of Pt2Cl n (2 ≤ n ≤ 10) Clusters

Laser ablation mass spectrometry was applied to study the cluster anions of Pt₂Cl _n^-. Among them, Pt₂Cl₆^- and Pt₂Cl₉^- were observed with remarkable intensities in the mass spectrum. Collision-activated dissociation experiments were also performed for the two anions. A systematic study of the structures and electron affinities (EAs) of Pt_1-2Cl _n (2 ≤ n ≤ 10) clusters was performed on the level of B3LYP/Lanl2dz/6-311++G(2d, p). For both systems, their EAs do not increase monotonically with the increase of Cl atoms. All the clusters of PtCl _n (3 ≤ n ≤ 10) and Pt₂Cl _n (3 ≤ n ≤ 10) show EAs larger than that of the Cl atom. The highest EAs for the series of Pt₂Cl _n and PtCl _n are 6.55 and 5.82 eV, corresponding to those of Pt₂Cl₉ and PtCl₉, respectively. The results indicate that these clusters might be applied as effective units in constructing new "hypersalts".

Near-Edge Soft X-ray Absorption Mass Spectrometry of Protonated Melittin

We have investigated the photoionization and photofragmentation yields of gas-phase multiply protonated melittin cations for photon energies at the K-shell absorption edges of carbon, nitrogen, and oxygen. Two similar experimental approaches were employed. In both experiments, mass selected [melittin+qH]^q+ (q=2-4) ions were accumulated in radiofrequency ion traps. The trap content was exposed to intense beams of monochromatic soft X-ray photons from synchrotron beamlines and photoproducts were analyzed by means of time-of-flight mass spectrometry. Mass spectra were recorded for fixed photon energies, and partial ion yield spectra were recorded as a function of photon energy. The combination of mass spectrometry and soft X-ray spectroscopy allows for a direct correlation of protein electronic structure with various photoionization channels. Non-dissociative single and double ionization are used as a reference. The contribution of both channels to various backbone scission channels is quantified and related to activation energies and protonation sites. Soft X-ray absorption mass spectrometry combines fast energy deposition with single and double ionization and could complement established activation techniques. Graphical Abstract ᅟ.

Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H+)2 and TLK(H+)2 fragmentation dynamics, and with thermal simulations

Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N₂, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.

Photodissociation spectroscopy of protonated leucine enkephalin

Protonated leucine enkephalin (YGGFL) was studied by ultraviolet photodissociation (UVPD) from 225 to 300 nm utilizing an optical parametric oscillator tunable wavelength laser system (OPO). Fragments were identified by absolute mass measurement in a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Bond cleavage was preferred in the vicinity of the two aromatic residues, resulting in high ion abundances for a₄, a₁, b₃, y₂ and y₁ fragments. a, b and y ions dominated the mass spectrum, and full sequence coverage was achieved for those types. Photodissociation was most effective at the short wavelength end of the studied range, which is assigned to the onset of the L_a π-π* transition of the tyrosine chromophore, but worked well also at the L_b π-π* chromophore absorption maxima in the 35 000-39 000 cm^-1 region. Several side-chain and internal fragments were observed. H atom loss is observed only above 41 000 cm^-1, consistent with the requirement of a curve crossing to a repulsive ¹πσ* state. It is suggested that the photochemically generated mobile H atom plays a role in further backbone cleavages, similar to the mechanism for electron capture dissociation. The b₄ fragment is most intense at the L_b chromophore absorptions, undergoing additional fragmentation at higher photon energies. The high resolution of the FT-ICR MS revealed that out of all x and z-type fragments only x₃ and x₄ were formed, with low intensity. Other previously reported x- and z-fragments were re-assigned to internal fragments, based on exact mass measurement.

The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein

Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.

Formation of endohedral metallofullerene (EMF) ions of MnC2m+ (M = La, Y, n ≤ 6, 50 ≤ 2m ≤ 194) in the laser ablation process with graphene as precursor

RATIONALE

Graphene has proved to be a versatile precursor for the generation of mono-endohedral metallofullerenes (EMFs) of alkali and alkali earth metal atoms. Thus, it is important to investigate whether graphene is also a good precursor for the generation of EMFs including multi-metal atoms or some transition metal atoms.

METHODS

Experiments were performed on a 7.0 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Laser ablation mass spectra were obtained by laser irradiation on mixtures of graphene and LaCl₃ , YCl₃ or HAuCl₄ on a stainless steel plate. A 355 nm Nd:YAG laser with a typical energy of 2.5 mJ/pulse was employed in these experiments. Tandem mass spectrometry was performed by on-resonance excitation collision-induced dissociation (CID) for selected single isotopic peaks.

RESULTS

Metallofullerene La1-6C2m+/ Y1-6C2m+ ions were observed in the laser ablation mass spectra of mixtures of graphene and LaCl₃ /YCl₃ . CID and reactant gas experiments on selected ions showed that these ions had endohedral structures. Considering the experimental condition applied here, a mechanism based on a top-down process for the generation of the EMF ions is suggested. Further experiments on HAuCl₄ showed some weak signals of AuC2m+ for the first time.

CONCLUSIONS

Mono- and multi-EMF ions of MnC2m+ (M = La, Y, n = 1-6, 50 ≤ 2 m ≤ 194) were generated by laser ablation of graphene and the corresponding metal salts and detected by FT-ICR mass spectrometry. The results have shed light on the formation and generation of some new EMF species. Copyright © 2017 John Wiley & Sons, Ltd.

Gas-phase reactivity of [Ca(formamide)]2+ complex: an example of different dynamical behaviours

In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)]²⁺ complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Multidimensional Mass Spectrometry of Synthetic Polymers and Advanced Materials

Multidimensional mass spectrometry interfaces a suitable ionization technique and mass analysis (MS) with fragmentation by tandem mass spectrometry (MS² ) and an orthogonal online separation method. Separation choices include liquid chromatography (LC) and ion-mobility spectrometry (IMS), in which separation takes place pre-ionization in the solution state or post-ionization in the gas phase, respectively. The MS step provides elemental composition information, while MS² exploits differences in the bond stabilities of a polymer, yielding connectivity and sequence information. LC conditions can be tuned to separate by polarity, end-group functionality, or hydrodynamic volume, whereas IMS adds selectivity by macromolecular shape and architecture. This Minireview discusses how selected combinations of the MS, MS² , LC, and IMS dimensions can be applied, together with the appropriate ionization method, to determine the constituents, structures, end groups, sequences, and architectures of a wide variety of homo- and copolymeric materials, including multicomponent blends, supramolecular assemblies, novel hybrid materials, and large cross-linked or nonionizable polymers.

Understanding ligand effects in gold clusters using mass spectrometry

This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because "each-atom-counts" toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well-defined surfaces may be explored using ion soft landing (SL) in a custom-built instrument combined with in situ time of flight secondary ion mass spectrometry (TOF-SIMS). Jointly, this multipronged experimental approach allows characterization of the full spectrum of relevant phenomena including cluster synthesis, ligand exchange, thermochemistry, surface immobilization, and reactivity. The fundamental insights obtained from this work will facilitate the directed synthesis of gold clusters with predetermined size and properties for specific applications.

Soft- and reactive landing of ions onto surfaces: Concepts and applications

Soft- and reactive landing of mass-selected ions is gaining attention as a promising approach for the precisely-controlled preparation of materials on surfaces that are not amenable to deposition using conventional methods. A broad range of ionization sources and mass filters are available that make ion soft-landing a versatile tool for surface modification using beams of hyperthermal (<100 eV) ions. The ability to select the mass-to-charge ratio of the ion, its kinetic energy and charge state, along with precise control of the size, shape, and position of the ion beam on the deposition target distinguishes ion soft landing from other surface modification techniques. Soft- and reactive landing have been used to prepare interfaces for practical applications as well as precisely-defined model surfaces for fundamental investigations in chemistry, physics, and materials science. For instance, soft- and reactive landing have been applied to study the surface chemistry of ions isolated in the gas-phase, prepare arrays of proteins for high-throughput biological screening, produce novel carbon-based and polymer materials, enrich the secondary structure of peptides and the chirality of organic molecules, immobilize electrochemically-active proteins and organometallics on electrodes, create thin films of complex molecules, and immobilize catalytically active organometallics as well as ligated metal clusters. In addition, soft landing has enabled investigation of the size-dependent behavior of bare metal clusters in the critical subnanometer size regime where chemical and physical properties do not scale predictably with size. The morphology, aggregation, and immobilization of larger bare metal nanoparticles, which are directly relevant to the design of catalysts as well as improved memory and electronic devices, have also been studied using ion soft landing. This review article begins in section 1 with a brief introduction to the existing applications of ion soft- and reactive landing. Section 2 provides an overview of the ionization sources and mass filters that have been used to date for soft landing of mass-selected ions. A discussion of the competing processes that occur during ion deposition as well as the types of ions and surfaces that have been investigated follows in section 3. Section 4 discusses the physical phenomena that occur during and after ion soft landing, including retention and reduction of ionic charge along with factors that impact the efficiency of ion deposition. The influence of soft landing on the secondary structure and biological activity of complex ions is addressed in section 5. Lastly, an overview of the structure and mobility as well as the catalytic, optical, magnetic, and redox properties of bare ionic clusters and nanoparticles deposited onto surfaces is presented in section 6.

UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry

De novo peptide sequencing by mass spectrometry represents an important strategy for characterizing novel peptides and proteins, in which a peptide's amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum (MS/MS or MS(3)) fragment ions, without comparison to a reference proteome. This method is ideal for organisms or samples lacking a complete or well-annotated reference sequence set. One of the major barriers to de novo spectral interpretation arises from confusion of N- and C-terminal ion series due to the symmetry between b and y ion pairs created by collisional activation methods (or c, z ions for electron-based activation methods). This is known as the "antisymmetric path problem" and leads to inverted amino acid subsequences within a de novo reconstruction. Here, we combine several key strategies for de novo peptide sequencing into a single high-throughput pipeline: high-efficiency carbamylation blocks lysine side chains, and subsequent tryptic digestion and N-terminal peptide derivatization with the ultraviolet chromophore AMCA yield peptides susceptible to 351 nm ultraviolet photodissociation (UVPD). UVPD-MS/MS of the AMCA-modified peptides then predominantly produces y ions in the MS/MS spectra, specifically addressing the antisymmetric path problem. Finally, the program UVnovo applies a random forest algorithm to automatically learn from and then interpret UVPD mass spectra, passing results to a hidden Markov model for de novo sequence prediction and scoring. We show this combined strategy provides high-performance de novo peptide sequencing, enabling the de novo sequencing of thousands of peptides from an Escherichia coli lysate at high confidence.

On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry

Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.

Medium-sized phosphorus cluster cations P+ 2m+1 (6 ≤ m ≤ 32) studied by collision-induced dissociation mass spectrometry

Medium-sized phosphorus cluster cations were generated by laser ablation of red phosphorus and investigated by the method of collision-induced dissociation mass spectrometry. Experimental results show that the primary dissociation channels of phosphorus cluster cations of P(+) 2m+1 (6 ≤ m ≤ 11) are all characterized by the loss of P4 unit. For larger cluster cations, their dissociation pathways were more complex. For those magic cations of P(+) 8k+1 observed previously, their dissociation pathways progressively change from the loss of P4 unit (for k = 3) to the loss of P8 unit (for k = 4, 5). A new dissociation pathway characterized by the loss of P10 unit was also indentified for larger cations of P(+) 8k+1 (6 ≤ k ≤ 8). Theoretical calculation also shows that, for cations of P(+) 2m+1 (4 ≤ m ≤ 10), the dissociation channel characterized by the loss of P4 unit is more energetically favorable than other dissociation channels, which is in good agreement with the experimental results.

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

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

Generation of M@C(2n)+ (M = K, Rb, Cs, 2n = 80-220) by laser ablation of graphene

RATIONALE

The yield of endohedral metallofullerene (EMF) ions is greatly related to the encaged metal atoms. For alkali metals, the generation of corresponding large-sized monometallofullerene ions by traditional methods is still difficult. The aim of this work is to study the generation and the distribution of alkali-metallofullerene ions by the method of laser ablation with graphene as the precursor.

METHODS

The experiment was performed with a Fourier transform ion cyclotron (FTICR) mass spectrometer. Mass spectra were obtained by laser ablation of the mixtures of graphene and KCl, RbCl or CsCl in the positive ion mode. Collision-induced dissociation (CID) experiments were also performed for some selected ions.

RESULTS

EMF ions of M@C(2n)+ (M = K, Rb, Cs, 2n = 80-220) can be generated by using graphene as the precursor. Other EMF ions with smaller sizes, including M@C60+, were also observed under the optimized experimental conditions. CID experiments of some selected ions confirmed their endohedral structures.

CONCLUSIONS

Metallofullerene ions of M@C(2n)+ (M = K, Rb, Cs, 2n = 80-220) were generated by laser ablation of graphene and corresponding metal salts. Compared with previous results of alkaline earth metals, the yields of EMF ions are generally lower. However, for large-sized EMF ions, the relative intensities of EMF ions to their corresponding fullerene ions I(M@C(2n)+)/ I(C(2n)+) generally increase with the increase in cluster sizes, which is opposite to the trend observed for alkaline earth metals.

Interactions of hemoglobin and myoglobin with their ligands CN(-), CO, and O2 monitored by electrospray ionization-mass spectrometry

Electrospray ionization (ESI)-mass spectrometry (MS) can provide information on protein-ligand interactions via detection of the corresponding complexes as gaseous ions. Unfortunately, some systems are prone to dissociation upon transfer into the gas phase. The reversible oxygen binding to hemoglobin (Hb) has been extensively studied in solution using a wide range of biophysical techniques. In addition to O2, ferrous (Fe(II)) Hb can bind CO. High affinity interactions with CN(-) are limited to the ferric (Fe(III)) state. In analogous fashion, CN(-), CO, and O2 bind to myoglobin (Mb). It remains unclear whether any of these ligand-bound forms can be observed by ESI-MS. In this work we demonstrate the successful detection of MbCN, while MbCO and MbO2 do not survive under ESI-MS conditions. Control experiments suggest that an older report of "MbO2" detection by ESI-MS may involve the misassignment of oxidation artifacts formed under corona discharge conditions. The situation is more favorable for ESI-MS studies on Hb. The most intense signal in the HbCN mass distribution corresponds to the expected complex with four cyanide moieties bound. Ligand loss during ESI-MS is around 20%. HbCO is detectable as well, albeit with a more noticeable level of ligand dissociation (∼50%) which produces the 2CO-bound state as the highest intensity ion in the spectrum. In addition, our data suggest that low levels of HbO2 can survive the transition into the gas phase, evident from +64 Da and +128 Da signals that can be assigned to Hb carrying two and four oxygen molecules, respectively. The application of collisional activation induces neutral ligand loss for all three Hb derivatives. It appears that this is the first report on the detection of MbCN, HbCO, and HbO2 in the gas phase. We hope that this work will pave the way towards future spectroscopic investigations of desolvated Mb and Hb, complementing the extensive literature on CN(-), CO, and O2 bound globins in the condensed phase.

Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides

In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types (a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide-M(2+) (M = Ca, Sr)

A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.

On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)ⁿ⁺ and (M−nH)ⁿ⁻ ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage.

Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies

Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0  = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡)  = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.

An IMS-IMS threshold method for semi-quantitative determination of activation barriers: Interconversion of proline cis↔trans forms in triply protonated bradykinin

Collisional activation of selected conformations by multidimensional ion mobility spectrometry (IMS-IMS), combined with mass spectrometry (MS), is described as a method to determine semi-quantitative activation energies for interconversion of different structures of the nonapeptide bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg). This analysis is based on a calibration involving collision-induced dissociation measurements of ions with known dissociation energies (i.e., "thermometer" ions) such as leucine enkephalin, BK, and amino acid-metal cation systems. The energetic barriers between six conformations of [BK+3H]3+ range from 0.23 ±0.01 to 0.55 ±0.03 eV. Prior results indicate that the major peaks in the IMS distributions correspond to specific combinations of cis and trans configurations of the three proline residues in the peptide sequence. The analysis allows us to directly assess pathways for specific transitions. The combination of structural assignments, experimentally determined barrier heights, onset of the quasi-equilibrium region, and dissociation threshold are used to derive a semi-quantitative potential energy surface for main features of [BK+3H]3+.

Collision cross section measurements for biomolecules within a high-resolution FT-ICR cell: theory

An energetic hard-sphere collision model for modern high-resolution FT-ICR.

Guanine tetrads: an IRMPD spectroscopy, energy resolved SORI-CID, and computational study of M(9-ethylguanine)4+ (M = Li, Na, K, Rb, Cs) in the gas phase

The electrostatic potential map of the neutral guanine tetrad showing the negative hole in the centre.

Identifying Ca2+-binding sites in proteins by liquid chromatography-mass spectrometry using Ca2+-directed dissociations

Here we describe a new method to identify calcium-binding sites in proteins using high-resolution liquid chromatography-mass spectrometry in concert with calcium-directed collision-induced dissociations. Our method does not require any modifications to the liquid chromatography-mass spectrometry apparatus, uses standard digestion protocols, and can be applied to existing high-resolution MS data files. In contrast to NMR, our method is applicable to very small amounts of complex protein mixtures (femtomole level). Calcium-bound peptides can be identified using three criteria: (1) the calculated exact mass of the calcium containing peptide; (2) specific dissociations of the calcium-containing peptide from threonine and serine residues; and (3) the very similar retention times of the calcium-containing peptide and the free peptide.

Dissociation of the anthracene radical cation: a comparative look at iPEPICO and collision-induced dissociation mass spectrometry results

The dissociation of the anthracene radical cation has been studied using two different methods: imaging photoelectron photoion coincidence spectrometry (iPEPCO) and atmospheric pressure chemical ionization-collision induced dissociation mass spectrometry (APCI-CID). Four reactions were investigated: (R1) C14H10(+•) → C14H9(+) + H, (R2) C14H9(+) → C14H8(+•) + H, (R3) C14H10(+•) → C12H8(+•) + C2H2 and (R4) C14H10(+•) → C10H8(+•) + C4H2. An attempt was made to assign structures to each fragment ion, and although there is still room for debate whether for the C12H8(+•) fragment ion is a cyclobuta[b]naphthalene or a biphenylene cation, our modeling results and calculations appear to suggest the more likely structure is cyclobuta[b]naphthalene. The results from the iPEPICO fitting of the dissociation of ionized anthracene are E0 = 4.28 ± 0.30 eV (R1), 2.71 ± 0.20 eV (R2), and 4.20 ± 0.30 eV (average of reaction R3) whereas the Δ(‡)S values (in J K(-1) mol(-1)) are 12 ± 15 (R1), 0 ± 15 (R2), and either 7 ± 10 (using cyclobuta[b]naphthalene ion fragment in reaction R3) or 22 ± 10 (using the biphenylene ion fragment in reaction R3). Modeling of the APCI-CID breakdown diagrams required an estimate of the postcollision internal energy distribution, which was arbitrarily assumed to correspond to a Boltzmann distribution in this study. One goal of this work was to determine if this assumption yields satisfactory energetics in agreement with the more constrained and theoretically vetted iPEPICO results. In the end, it did, with the APCI-CID results being similar.

In situ SIMS and IR spectroscopy of well-defined surfaces prepared by soft landing of mass-selected ions

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3](2+) (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.

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](•+).

157 nm photodissociation of dipeptide ions containing N-terminal arginine

Twenty singly-charged dipeptide ions with N-terminal arginine were photodissociated using 157 nm light in both a linear ion-trap mass spectrometer and a MALDI-TOF-TOF mass spectrometer. Analogous to previous work on dipeptides containing C-terminal arginine, this set of samples enabled insights into the photofragmentation propensities associated with individual residues. In addition to familiar products such as a-, d-, and immonium ions, m2 and m2+13 ions were also observed. Certain side chains tended to cleave between their β and γ carbons without necessarily forming d- or w-type ions, and a few other ions were produced by the high-energy fragmentation of multiple bonds.

Top-down proteomics by means of Orbitrap mass spectrometry

Top-down proteomics has become a popular approach for the analysis of intact proteins. The term "top down" has been coined for the analysis of proteins not involving any enzymatic or chemical cleavage but rather the ionization of the protein as a sound molecule and mass analysis of intact species and fragment ions thereof produced upon dissociation inside a mass spectrometer. One or several charge states of the protein are mass-isolated and subjected to dissociation (MS/MS) in the gas phase. The obtained fragment masses, predominantly from cleavages of the protein along its amino acid backbone, are directly related to the intact protein. Using bioinformatics tools the fragment masses are matched against a known protein sequence or can alternatively be used for partial or full de novo sequencing, depending on the size of the protein and the number of fragment ions obtained. Moreover, this approach provides global information about modification states of proteins including the number and types of isoforms and their stoichiometry and allows for the precise localization of modifications within the amino acid sequence. Top-down analysis of a single, purified protein can be performed by matrix-assisted laser desorption ionization or electrospray ionization upon direct infusion without online chromatographic separation, whereas top-down analysis of complex protein mixtures makes pre-fractionation combined with an efficient front-end chromatographic separation coupled online to the mass spectrometer inevitable.

De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry

Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.

Selective 351 nm photodissociation of cysteine-containing peptides for discrimination of antigen-binding regions of IgG fragments in bottom-up liquid chromatography-tandem mass spectrometry workflows

Despite tremendous inroads in the development of more sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies for mass spectrometry-based proteomics, there remains a significant need for enhancing the selectivity of MS/MS-based workflows for streamlined analysis of complex biological mixtures. Here, a novel LC-MS/MS platform based on 351 nm ultraviolet photodissociation (UVPD) is presented for the selective analysis of cysteine-peptide subsets in complex protein digests. Cysteine-selective UVPD is mediated through the site-specific conjugation of reduced cysteine residues with a 351 nm active chromogenic Alexa Fluor 350 (AF350) maleimide tag. Only peptides containing the AF350 chromophore undergo photodissociation into extensive arrays of b- and y-type fragment ions, thus providing a facile means for differentiating cysteine-peptide targets from convoluting peptide backgrounds. With the use of this approach in addition to strategic proteolysis, the selective analysis of diagnostic heavy-chain complementarity determining regions (CDRs) of single-chain antibody (scAb) fragments is demonstrated.

157 nm photodissociation of a complete set of dipeptide ions containing C-terminal arginine

Twenty singly-charged dipeptide ions with C-terminal arginine were photodissociated with 157 nm light and their tandem mass spectra recorded. Many of the small product ions that were observed are standard peptide fragments that have been commonly seen in VUV photodissociation studies. However, the study of a library of dipeptides containing all 20 N-terminal amino acids enabled the recognition of trends associated with the occurrence of w-, v-, and immonium ions, the observation of competition between forming N- and C-terminal fragments in dipeptide RR, and the identification of some unusual fragment ions appearing at masses of 183, 187, 196, and 197 Da. A highly accurate internal calibration of the photodissociation TOF-TOF data enabled molecular formulae for these four product ions to be derived. Their proposed structures reflect the rather high-energy nature of this fragmentation phenomenon.

Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains

RATIONALE

The hypothesis that dissociation energies can serve as a predictor of observability of b- and y-peaks is tested for seven hexapeptides. If the hypothesis holds true for large classes of peptides, one would be able to improve the scoring accuracy of peptide identification tools by excluding theoretical peaks that cannot be observed in practical product ion spectra due to various physical, chemical or thermodynamic considerations.

METHODS

Product ion m/z spectra of hexapeptides AAAAAA, AAAFAA, AAAVAA, AAFAAA, AAVAAA, AAFFAA and AAVVAA have been acquired on a Finnigan LTQ XL mass spectrometer in the collision-induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. Dissociation energies were calculated for all fragmentation channels leading to b- and y-fragments at the TPSS/6-31G(d,p) level of the density functional theory.

RESULTS

It was demonstrated that the m/z peaks observed in the product ion spectra correspond to the fragmentation channels with dissociation energies below a certain threshold value. However, there is no direct correlation between the most intense m/z peaks and the lowest dissociation energies. Using the dissociation energies, it was predicted that out of 63 theoretically possible peaks in the b- and y-series of the seven hexapeptides, 19 should not be observable in practical spectra. In the experiments, 24 peaks were not observed, including all 19 predicted.

CONCLUSIONS

Dissociation energies alone are not sufficient for predicting ion intensity relationships in product ion m/z spectra. Nevertheless, the present data suggest that dissociation energies appear to be good predictors of observability of b- and y-peaks and potentially very useful for filtering theoretical peaks of each candidate peptide in peptide identification tools. Published 2012. This article is a US Government work and is in the public domain in the USA.