Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry.

Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.

Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation.

One challenge associated with the discovery and development of monoclonal antibody (mAb) therapeutics is the determination of heavy chain and light chain pairing. Advances in MS instrumentation and MS/MS methods have greatly enhanced capabilities for the analysis of large intact proteins yielding much more detailed and accurate proteoform characterization. Consequently, direct interrogation of intact antibodies or F(ab')2 and Fab fragments has the potential to significantly streamline therapeutic mAb discovery processes. Here, we demonstrate for the first time the ability to efficiently cleave disulfide bonds linking heavy and light chains of mAbs using electron capture dissociation (ECD) and 157 nm ultraviolet photodissociation (UVPD). The combination of intact mAb, Fab, or F(ab')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain and light chain pairing from a single experiment and experimental condition. These results demonstrate the potential of top-down and middle-down proteomics to significantly streamline therapeutic antibody discovery.

Sequencing Grade Tandem Mass Spectrometry for Top-Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer.

Compared to traditional collision induced dissociation methods, electron capture dissociation (ECD) provides more comprehensive characterization of large peptides and proteins as well as preserves labile post-translational modifications. However, ECD experiments are generally restricted to the high magnetic fields of FTICR-MS that enable the reaction of large polycations and electrons. Here, we demonstrate the use of an electromagnetostatic ECD cell to perform ECD and hybrid ECD methods utilizing 193 nm photons (ECuvPD) or collisional activation (EChcD) in a benchtop quadrupole-Orbitrap mass spectrometer. The electromagnetostatic ECD cell was designed to replace the transfer octapole between the quadrupole and C-trap. This implementation enabled facile installation of the ECD cell, and ions could be independently subjected to ECD, UVPD, HCD, or any combination. Initial benchmarking and characterization of fragmentation propensities for ECD, ECuvPD, and EChcD were performed using ubiquitin (8.6 kDa). ECD yielded extensive sequence coverage for low charge states of ubiquitin as well as for the larger protein carbonic anhydrase II (29 kDa), indicating pseudo-activated ion conditions. Additionally, relatively high numbers of d- and w-ions enable differentiation of isobaric isoleucine and leucine residues and suggest a distribution of electron energies yield hot-ECD type fragmentation. We report the most comprehensive characterization to date for model proteins up to 29 kDa and a monoclonal antibody at the subunit level. ECD, ECuvPD, and EChcD yielded 93, 95, and 91% sequence coverage, respectively, for carbonic anhydrase II (29 kDa), and targeted online analyses of monoclonal antibody subunits yielded 86% overall antibody sequence coverage.

Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer.

As the application of mass spectrometry intensifies in scope and diversity, the need for advanced instrumentation addressing a wide variety of analytical needs also increases. To this end, many modern, top-end mass spectrometers are designed or modified to include a wider range of fragmentation technologies, for example, ECD, ETD, EThcD, and UVPD. Still, the majority of instrument platforms are limited to more conventional methods, such as CID and HCD. While these latter methods have performed well, the less conventional fragmentation methods have been shown to lead to increased information in many applications including middle-down proteomics, top-down proteomics, glycoproteomics, and disulfide bond mapping. We describe the modification of the popular Q Exactive Orbitrap mass spectrometer to extend its fragmentation capabilities to include ECD. We show that this modification allows ≥85% matched ion intensity to originate from ECD fragment ion types as well as provides high sequence coverage (≥60%) of intact proteins and high fragment identification rates with ∼70% of ion signals matched. Finally, the ECD implementation promotes selective disulfide bond dissociation, facilitating the identification of disulfide-linked peptide conjugates. Collectively, this modification extends the capabilities of the Q Exactive Orbitrap mass spectrometer to a range of new applications.

Characterization and Identification of Dityrosine Cross-Linked Peptides Using Tandem Mass Spectrometry.

The use of mass spectrometry coupled with chemical cross-linking of proteins has become a powerful tool for proteins structure and interactions studies. Unlike structural analysis of proteins using chemical reagents specific for lysine or cysteine residues, identification of gas-phase fragmentation patterns of endogenous dityrosine cross-linked peptides have not been investigated. Dityrosine cross-linking in proteins and peptides are clinical markers of oxidative stress, aging, and neurodegenerative diseases including Alzheimer's disease and Parkinson's disease. In this study, we investigated and characterized the fragmentation pattern of a synthetically prepared dityrosine cross-linked dimer of Aß(1-16) using ESI tandem mass spectrometry. We then detailed the fragmentation pattern of dityrosine cross-linked Aß(1-16), using collision induced dissociation (CID), higher-energy collision induced dissociation (HCD), electron transfer dissociation (ETD), and electron capture dissociation (ECD). Application of these generic fragmentation rules of dityrosine cross-linked peptides allowed for the identification of dityrosine cross-links in peptides of Aß and α-synuclein generated in vitro by enzymatic peroxidation. We report, for the first time, the dityrosine cross-linked residues in human hemoglobin and α-synuclein under oxidative conditions. Together these tools open up the potential for automated analysis of this naturally occurring post-translation modification in neurodegenerative diseases as well as other pathological conditions.

Protein modifications by electrophilic lipoxidation products: adduct formation, chemical strategies and tandem mass spectrometry for their detection and identification.

The post-translational modification of proteins by electrophilic oxylipids is emerging as an important mechanism that contributes to the complexity of proteomes. Enzymatic and non-enzymatic oxidation of biological lipids results in the formation of chemically diverse electrophilic carbonyl compounds, such as 2-alkenals and 4-hydroxy alkenals, epoxides, and eicosanoids with reactive cyclopentenone structures. These lipoxidation products are capable of modifying proteins. Originally considered solely as markers of oxidative insult, more recently the modifications of proteins by lipid peroxidation products are being recognized as a new mechanism of cell signaling with relevance to redox homeostasis, adaptive response and inflammatory resolution. The growing interest in protein modifications by reactive oxylipid species necessitates the availability of methods that are capable of detecting, identifying and characterizing these protein adducts in biological samples with high complexity. However, the efficient analysis of these chemically diverse protein adducts presents a considerable analytical challenge. We first provide an introduction into the chemistry and biological relevance of protein adductions by electrophilic lipoxidation products. We then provide an overview of tandem mass spectrometry approaches that have been developed in recent years for the interrogation of protein modifications by electrophilic oxylipid species.

High resolution mass analysis of N- and C-terminal negative ions resulting from resonance electron capture by aliphatic amino acids.

High mass resolving power was applied to study resonance electron capture by glycine, alanine, and valine, and accurate mass measurements helped to distinguish between some negative ions having the same nominal masses. It was established that the C- and N-terminal negative ions of the same nominal masses were formed at different electron energies from different resonance states. The typical fragmentation pathways in deprotonated amino acids via loss of water initiated by collisional activation were not observed upon resonant electron capture by aliphatic amino acids. Instead, [M-18](-) negative ions in the vicinity of 5 eV were found to be associated with simultaneous loss of either ammonia and a hydrogen atom or an amino group and a hydrogen molecule.

Resonance electron capture by serine.

Formation of negative ions via dissociative electron attachment (DEA) to the amino acid serine in the gas phase was studied using two different crossed electron/molecular beam techniques and quantum chemical calculations. Resonance electron capture mass spectrum and effective ion yield curves of 16 negative ions were measured over the electron energy range from close to 0 to 11 eV. The negative ions from serine were detected from resonance states in the vicinity of 0, 1.3, 5, and 8 eV. The dominant reaction channel at low electron energies was (M-H)(-). The relative cross section for this ion exceeds more than 20 times that of any other fragment negative ions. A high-resolution experiment was applied to study fine structures in (M-H)(-) cross section. We have found that the second OH group influences some dissociative channels. Quantum chemical calculations were applied to interpret products of the DEA reaction channels.

Fragmentation of peptide negative molecular ions induced by resonance electron capture.

A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z(n)-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H](-) NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c(n)+1 ions. Instead, c(n) ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z(n)-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c(n) ions than for the z(n)-1 ions. The mechanisms for the N-C(alpha) bond cleavage are discussed.

Resonant electron capture by some amino acids esters.

Resonant electron capture by Gly, Ala and Phe esters have shown that the most efficient negative ion (NI) fragmentations are associated with the C-termini. A new mechanism for the negative ion-forming processes at energies lower than those associated with the pi*(OO) shape resonance involves coupling between dipole-bound and valence negative ion states of the same symmetry for amino acid conformers with high permanent dipoles. The interaction avoids crossing of the NI states and instead leads to formation of two adiabatic potential energy surfaces. Underivatized amino acids most effectively fragment from the bottom adiabatic surface via generation of [M-H](-) carboxylate anions by hydrogen-atom tunneling through the barrier; fragmentation of the their esters with formation of analogues [M-X](-) NIs occurs through the upper adiabatic state without penetration of the barrier in which the energy of the valence sigma*OX resonance exceeds the bond dissociation energy of the neutral molecule. Low and high temperature resonant electron capture experiments point to the importance of conformational preferences of the amino acids for optimum dissociation of the parent NIs in the gas phase.

Electron transfer reactivity in matrix-assisted laser desorption/ionization (MALDI): ionization energy, electron affinity and performance of the DCTB matrix within the thermochemical framework.

DCTB [(H(3)C)(3)C-p-Ph-CH=C(CH(3))-trans-CH=C(CN)(2)] has recently advanced to the most promising matrix material for matrix-assisted laser desorption/ionization (MALDI) within material sciences. However, data that would allow the evaluation of the electron-transfer reactivity within a thermochemical framework are sparse. The present study reports the first-time determination of the ionization energy (IE) of DCTB applying photoelectron (PE) spectroscopy. The experimental IE (8.54 +/- 0.05 eV) is in excellent agreement with the theoretical value of 8.47 eV, obtained by AM1 calculations. The same level of theory determines the electron affinity (EA) as 2.31 eV. Model analytes of known thermochemistry (phenanthrene [C(14)H(10)], anthracene [C(14)H(10)] and fluorofullerene [C(60)F(46/48)]) are used to bracket the electron-transfer reactivity within DCTB-MALDI. The formation of molecular ions of these analytes either is expected or is beyond the thermochemical accessibility of the DCTB matrix.

Resonant electron capture by some amino acids and their methyl esters.

Resonant electron capture mass spectra of aliphatic and aromatic amino acids and their methyl esters show intense [M-H](-) negative ions in the low-energy range. Ion formation results from a predissociation mechanism mediated by the low-energy pi*oo resonant state. Methylation in general has little influence on the electronic structure according to quantum chemical calculations, but the corresponding ions from the methyl esters, [M-Me](-), could be ascertained to arise only at higher resonance energies. Aromatic amino acids are characterized by an additional low-energy fragmentation channel associated with the generation of negative ions with loss of the side chain. The complementary negative ions of the side chains are more efficiently produced at higher energies. The results have significant implications in biological systems as they suggest that amino acids can serve as radiation protectors since they have been found to efficiently thermalize electrons.

Application and evaluation of solvent-free matrix-assisted laser desorption/ionization mass spectrometry for the analysis of derivatized fullerenes.

A variety of derivatized fullerenes have been studied by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Of particular emphasis has been the evaluation of a recently introduced solvent-free sample/target preparation method. Solvent-free MALDI is particularly valuable in overcoming adverse solvent-related effects, such as insolubility and/or degradation of the sample. The method was applied to fullerene derivatives susceptible to decomposition under insufficiently "soft" MALDI conditions. Analytes included the hydrofullerene: C(60)H(36), fluorofullerenes: C(60)F(x) where x = 18, 36, 46, 48 and C(70)F(x) where x = 54, 56, methano-bridged amphiphilic ligand adducts to C(60) and the [4 + 2] cycloadduct of tetracene to C(60). The new solvent-free sample preparation is established as an exceedingly valuable addition to the repertoire of preparation protocols within MALDI. The MALDI mass spectra were of very high quality throughout, providing a testimony that "soft" MALDI conditions could be achieved. Using the [4 + 2] cycloadduct of tetracene to C(60) as the model analyte for direct comparison with solvent-based MALDI, the solvent-free approach led to less fragmentation and more abundant analyte ions. Applying solvent-free sample preparation, different matrix compounds have been examined for use in the MALDI of derivatized fullerenes, including sulfur, tetracyanoquinodimethane (TCNQ), 9-nitroanthracene (9-NA) and trans-2-[3-(4-tert-butylphenyl)-2-methyl-2- propenylidene]malononitrile (DCTB). DCTB was confirmed as the best performing matrix, reducing unwanted decomposition and suppression effects.

Bulk production of a strong covalently linked (C60H(x))2 dimer.

The high-pressure treatment of C60 in an H2 atmosphere at high temperatures leads to the efficient formation of a covalently bound dimer and some oligomeric species. The resulting hydrogenated C120 is an example of the bulk production of covalently bound derivatized fullerene cores. Matrix-assisted laser desorption/ionization in conjunction with reflectron time-of-flight mass spectrometry has been applied to the product analysis. The dissociation pattern of selected C120H(2x)+ ions (x > 30) indicates the dimeric structure of (C60H(x))2, as opposed to a giant hydrofullerene species possessing a fused C120 core. However, the results also clearly indicate a much stronger bonding (multiple sigma bonding) between the C60H(x) units than present in cycloaddition products. Evidence of a covalently linked dimer was obtained in labeling experiments, on the basis of which any laser-induced gas-phase aggregation of the C60H(x) monomer during the analysis is discounted.

Hydrogen storage on fullerenes: hydrogenation of C59N. using C60H36 as the source of hydrogen.

C(60)H(36) has been used as the source of hydrogen for the in situ hydrogenation of (C(59)N)(2), leading to C(59)NH(5) as the main reaction product identified by negative-ion mass spectrometry and providing evidence of the usage of C(60) as a storage device for hydrogen.

A resonant electron capture time-of-flight MS with trochoidal electron monochromator.

A prototype electron monochromator (EM) reflectron time-of-flight (TOF) mass spectrometer has been constructed and demonstrated to record resonant electron capture (REC) mass spectra of electron-capturing compounds. The electron energy is ramped from -1.7 to +25 eV at a preset frequency, and the energy spread of the electron beam at 15 nA is 100 meV or better. Ions are orthogonally extracted into the analyzer at a frequency of up to 80 kHz while maintaining an upper m/z-limit of at least 300 and a mass resolving power of approximately 1000. A complete REC mass spectrum, which includes an effective yield versus electron energy curve for each negative ion formed from the compound being analyzed, typically takes several days to produce with a quadrupole or magnetic sector mass spectrometer. With the EM TOF described in this work, three-dimensional negative ion electron capture spectra are recorded in an interval on the order of only 1 s and displayed in real time. This new analytical capability could make it possible to perform GC REC mass spectrometry as well as easier (a) to measure the temperature dependence of REC cross sections, (b) to determine enthalpies of negative ion formation (accurate determination of the enthalpy of ion formation requires knowledge of the translational energy released during a dissociative capture event), and (c) to provide complete thermochemical descriptions of dissociative electron attachment by measuring ion lifetimes.