Top-down mass spectrometry analysis of capsid proteins of recombinant adeno-associated virus using multiple ion activations and proton transfer charge reduction.

Adeno-associated viruses (AAVs) are common vectors for emerging gene therapies due to their lack of pathogenicity in humans. Here, we present our investigation of the viral proteins (i.e., VP1, VP2, and VP3) of the capsid of AAVs via top-down mass spectrometry (MS). These proteins, ranging from 59 to 81 kDa, were chromatographically separated using hydrophilic interaction liquid chromatography and characterized in the gas-phase by high-resolution Orbitrap Fourier transform MS. Complementary ion dissociation methods were utilized to improve the overall sequence coverage. By reducing the overlap of product ion signals via proton transfer charge reduction on the Orbitrap Ascend BioPharma Tribrid mass spectrometer, the sequence coverage of each VP was significantly increased, reaching up to ∼40% in the case of VP3. These results showcase the improvements in the sequencing of proteins >30 kDa that can be achieved by manipulating product ions via gas-phase reactions to obtain easy-to-interpret fragmentation mass spectra.

Hydrophilic Interaction Chromatography Coupled to Ultraviolet Photodissociation Affords Identification, Localization, and Relative Quantitation of Glycans on Intact Glycoproteins.

Protein glycosylation is implicated in a wide array of diseases, yet glycoprotein analysis remains elusive owing to the extreme heterogeneity of glycans, including microheterogeneity of some of the glycosites (amino acid residues). Various mass spectrometry (MS) strategies have proven tremendously successful for localizing and identifying glycans, typically utilizing a bottom-up workflow in which glycoproteins are digested to create glycopeptides to facilitate analysis. An emerging alternative is top-down MS that aims to characterize intact glycoproteins to allow precise identification and localization of glycans. The most comprehensive characterization of intact glycoproteins requires integration of a suitable separation method and high performance tandem mass spectrometry to provide both protein sequence information and glycosite localization. Here, we couple ultraviolet photodissociation and hydrophilic interaction chromatography with high resolution mass spectrometry to advance the characterization of intact glycoproteins ranging from 15 to 34 kDa, offering site localization of glycans, providing sequence coverages up to 93%, and affording relative quantitation of individual glycoforms.

Native Mass Spectrometry Reveals Binding Interactions of SARS-CoV-2 PLpro with Inhibitors and Cellular Targets.

Here we used native mass spectrometry (native MS) to probe a SARS-CoV protease, PLpro, which plays critical roles in coronavirus disease by affecting viral protein production and antagonizing host antiviral responses. Ultraviolet photodissociation (UVPD) and variable temperature electrospray ionization (vT ESI) were used to localize binding sites of PLpro inhibitors and revealed the stabilizing effects of inhibitors on protein tertiary structure. We compared PLpro from SARS-CoV-1 and SARS-CoV-2 in terms of inhibitor and ISG15 interactions to discern possible differences in protease function. A PLpro mutant lacking a single cysteine was used to localize inhibitor binding, and thermodynamic measurements revealed that inhibitor PR-619 stabilized the folded PLpro structure. These results will inform further development of PLpro as a therapeutic target against SARS-CoV-2 and other emerging coronaviruses.

Reactions of Aluminum Oxide Cluster Cations with Ethane: A Mass-Spectrometric and Vibrational Spectroscopy Study.

The pathways for the reactions of aluminum oxide cluster ions with ethane have been measured. For selected ions (Al2O+, Al3O2+, Al3O4+, Al4O7+) the structure of the collisionally-stabilized reaction intermediates were explored by measuring the photodissociation vibrational spectra from 2600 cm-1 to 3100 cm-1. Density functional theory was used to calculate features of the potential energy surfaces for the reactions and the vibrational spectra of intermediates. Generally, more than one isomer contributes to the observed spectrum. The oxygen-deficient clusters Al2O+ and Al3O2+ have large C-H activation barriers, so only the entrance channel complexes in which intact C2H6 binds to aluminum are observed. This interaction leads to a substantial (~200 cm-1) red shift of the C-H symmetric stretch in ethane, indicating significant weakening of the proximal C-H bonds. In Al3O4+, the complex formed by interactions with three C2H6 is investigated and, in addition to entrance channel complexes, the C-H activation intermediate Al3O4H+(C2H5)(C2H6)2 is observed. For oxygen-rich Al4O7+, the C2H6 is favored to bind at an aluminum site far from the reactive superoxide group, reducing the reactivity. As expected, oxygen-rich species and open-shell cluster ions have smaller barriers for C-H bond activation, except for Al3O4+ which is predicted and observed to be reactive.

Ru-terpyridine complexes containing clotrimazole as potent photoactivatable selective antifungal agents.

The overuse of antimicrobial agents in medical and veterinary applications has led to the development of antimicrobial resistance in some microorganisms and this is now one of the major concerns in modern society. In this context, the use of transition metal complexes with photoactivatable properties, which can act as drug delivery systems triggered by light, could become a potent strategy to overcome the problem of resistance. In this work several Ru complexes with terpyridine ligands and the clotrimazole fragment, which is a potent antimycotic drug, were synthesized. The main goal was to explore the potential photoactivated activity of the complexes as antifungal agents and evaluate the effect of introducing different substituents on the terpyridine ligand. The complexes were capable of delivering the clotrimazole unit upon irradiation with visible light in a short period of time. The influence of the substituents on the photodissociation rate was explained by means of TD-DFT calculations. The complexes were tested against three different yeasts, which were selected based on their prevalence in fungal infections. The complex in which a carboxybenzene unit was attached to the terpyridine ligand showed the best activity against the three species under light, with minimal inhibitory concentration values of 0.88 µM and a phototoxicity index of 50 achieved. The activity of this complex was markedly higher than that of free clotrimazole, especially upon irradiation with visible light (141 times higher). The complexes were more active on yeast species than on cancer cell lines.

Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry.

Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods─namely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation─in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns.

Structural characterization of wax esters using ultraviolet photodissociation mass spectrometry.

Wax esters play critical roles in biological systems, serving functions from energy storage to chemical signaling. Their diversity is attributed to variations in alcohol and acyl chains, including their length, branching, and the stereochemistry of double bonds. Traditional analysis by mass spectrometry with collisional activations (CID, HCD) offers insights into acyl chain lengths and unsaturation level. Still, it falls short in pinpointing more nuanced structural features like the position of double bonds. As a solution, this study explores the application of 213-nm ultraviolet photodissociation (UVPD) for the detailed structural analysis of wax esters. It is shown that lithium adducts provide unique fragments as a result of Norrish and Norrish-Yang reactions at the ester moieties and photoinduced cleavages of double bonds. The product ions are useful for determining chain lengths and localizing double bonds. UVPD spectra of various wax esters are presented systematically, and the effect of activation time is discussed. The applicability of tandem mass spectrometry with UVPD is demonstrated for wax esters from natural sources. The UHPLC analysis of jojoba oil proves the compatibility of MS2 UVPD with the chromatography time scale, and a direct infusion is used to analyze wax esters from vernix caseosa. Data shows the potential of UVPD and its combination with CID or HCD in advancing our understanding of wax ester structures.

[Applications of native mass spectrometry and ultraviolet photodissociation in protein structure and interaction analysis].

Dynamic changes in the structures and interactions of proteins are closely correlated with their biological functions. However, the precise detection and analysis of these molecules are challenging. Native mass spectrometry (nMS) introduces proteins or protein complexes into the gas phase by electrospray ionization, and then performs MS analysis under near-physiological conditions that preserve the folded state of proteins and their complexes in solution. nMS can provide information on stoichiometry, assembly, and dissociation constants by directly determining the relative molecular masses of protein complexes through high-resolution MS. It can also integrate various MS dissociation technologies, such as collision-induced dissociation (CID), surface-induced dissociation (SID), and ultraviolet photodissociation (UVPD), to analyze the conformational changes, binding interfaces, and active sites of protein complexes, thereby revealing the relationship between their interactions and biological functions. UVPD, especially 193 nm excimer laser UVPD, is a rapidly evolving MS dissociation method that can directly dissociate the covalent bonds of protein backbones with a single pulse. It can generate different types of fragment ions, while preserving noncovalent interactions such as hydrogen bonds within these ions, thereby enabling the MS analysis of protein structures with single-amino-acid-site resolution. This review outlines the applications and recent progress of nMS and UVPD in protein dynamic structure and interaction analyses. It covers the nMS techniques used to analyze protein-small-molecule ligand interactions, the structures of membrane proteins and their complexes, and protein-protein interactions. The discussion on UVPD includes the analysis of gas-phase protein structures and interactions, as well as alterations in protein dynamic structures, and interactions resulting from mutations and ligand binding. Finally, this review describes the future development prospects for protein analysis by nMS and new-generation advanced extreme UV light sources with higher brightness and shorter pulses.

Infrared Photodissociation Spectroscopy of Dinuclear Vanadium-Group Metal Carbonyl Complexes: Diatomic Synergistic Activation of Carbon Monoxide.

The geometric structure and bonding features of dinuclear vanadium-group transition metal carbonyl cation complexes in the form of VM(CO)n+ (n = 9-11, M = V, Nb, and Ta) are studied by infrared photodissociation spectroscopy in conjunction with density functional calculations. The homodinuclear V2(CO)9+ is characterized as a quartet structure with CS symmetry, featuring two side-on bridging carbonyls and an end-on semi-bridging carbonyl. In contrast, for the heterodinuclear VNb(CO)9+ and VTa(CO)9+, a C2V sextet isomer with a linear bridging carbonyl is determined to coexist with the lower-lying CS structure analogous to V2(CO)9+. Bonding analyses manifest that the detected VM(CO)9+ complexes featuring an (OC)6M-V(CO)3 pattern can be regarded as the reaction products of two stable metal carbonyl fragments, and indicate the presence of the M-V d-d covalent interaction in the CS structure of VM(CO)9+. In addition, it is demonstrated that the significant activation of the bridging carbonyls in the VM(CO)9+ complexes is due in large part to the diatomic cooperation of M-V, where the strong oxophilicity of vanadium is crucial to facilitate its binding to the oxygen end of the carbonyl groups. The results offer important insight into the structure and bonding of dinuclear vanadium-containing transition metal carbonyl cluster cations and provide inspiration for the design of active vanadium-based diatomic catalysts.

A Coppoborylene Stabilized by Multicenter Covalent Bonding and Its Amphoteric Reactivity to CO.

A cationic copper-stabilized coppoborylene was prepared and structurally characterized via infrared photodissociation spectroscopy and density functional theory calculations. This structure exemplifies a new class of borylenes stabilized by three-center-two-electron metal-boron-metal covalent bonding interaction, displaying exceptional σ-acidity and unparalleled π-donor capability for CO activation that outperforms all of the known transition metal cations and is comparable or even superior to the documented base-trapped borylenes. Its neutral form represents a monovalent boron compound with a strongly reactive amphoteric boron center built on transition-metal-boron bonds, which inspires the design and synthesis of new members of the borylene family.

A Photoswitchable Metallocycle Based on Azobenzene: Synthesis, Characterization, and Ultrafast Dynamics.

The novel photoswitchable ligand 3,3'-Azobenz(metPA)2 (1) is used to prepare a [Cu2(1)2](BF4)2 metallocycle (2), whose photoisomerization was characterized using static and time-resolved spectroscopic methods. Optical studies demonstrate the highly quantitative and reproducible photoinduced cyclic E/Z switching without decay of the complex. Accordingly and best to our knowledge, [Cu2(1)2](BF4)2 constitutes the first reversibly photoswitchable (3d)-metallocycle based on azobenzene. The photoinduced multiexponential dynamics in the sub-picosecond to few picosecond time domain of 1 and 2 have been assessed. These ultrafast dynamics as well as the yield of the respective photostationary state (PSSZ = 65 %) resemble the behavior of archetypical azobenzene. Also, the innovative pump-probe laser technique of gas phase transient photodissociation (τ-PD) in a mass spectrometric ion trap was used to determine the intrinsic relaxation dynamics for the isolated complex. These results are consistent with the results from femtosecond UV/Vis transient absorption (fs-TA) in solution, emphasizing the azobenzene-like dynamics of 2. This unique combination of fs-TA and τ-PD enables valuable insights into the prevailing interplay of dynamics and solvation. Both analyses (in solution and gas phase) and quantum chemical calculations reveal a negligible effect of the metal coordination on the switching mechanism and electronic pathway, which suggests a non-cooperative isomerization process.

Photodissociation and formation of an ion-pair in CH2 FCl (HCFC-31).

Although CH2 FCl (HCFC-31) recently became of great atmospheric importance, studies concerning its excited states are almost nonexistent. Several excited singlet states were studied (valence nσ* and Rydberg n3s, n3p, σ3s, and σ3p) through highly correlated multireference configuration interaction with singles and doubles, including extensivity correction. Comparison with the states of CH3 Cl indicates a strong influence of the F atom. Potential energy curves suggest formation of an electrostatically bound complex that relaxes to a hydrogen-bonded contact ion-pair (HBCIP) which can decay yielding CH2 F + Cl or to the ground state minimum of CH2 FCl. The HBCIP has a dipole moment of 9.57 D, a CI wavefunction described as 0.65ionic + 0.20biradical and it is strongly bonded by 4.72 eV. Its H bond has characteristics of moderate and strong H bonds. The simulated absorption spectrum confirms the nσ* assignment for the first and suggests the n3s + n3pσ assignment for the second band.

Role of Triplet States in the Photolysis of Proteogenic Amino Acids.

This investigation delves into the UV photodissociation of pivotal amino acids (Alanine, Glycine, Leucine, Proline, and Serine) at 213 nm, providing insights into triplet-state deactivation pathways. Utilizing a comprehensive approach involving time-dependent density functional calculations (TD-DFT), multi-configurational methods, and ab-initio molecular dynamics (AIMD) simulations, we scrutinize the excited electronic states (T1 , T2 , and S1 ) subsequent to 213 nm excitation. Our findings demonstrate that α-carbonyl C-C bond-breaking in triplet states exhibits markedly lower barriers than in singlet states (below 5.0 kcal mol-1 ). AIMD simulations corroborate the potential involvement of triplet states in amino acid fragmentation, underscoring the significance of accounting for these states in photochemistry. Chemical bonding analyses unveil distinctive patterns for S1 and T1 states, with the asymmetric redistribution of electron density characterizing the C-C breaking in triplet states, in contrast to the symmetric breaking observed in singlet states. This research complements recent experimental discoveries, enhancing our comprehension of amino acid reactions in the interstellar medium.

Ultraviolet photodissociation and collision-induced dissociation for qualitative/quantitative analysis of low molecular weight compounds by liquid chromatography-mass spectrometry.

Collision-induced dissociation (CID) is the most wildly used fragmentation technique for qualitative and quantitative determination of low molecular weight compounds (LMWC). Ultraviolet photodissociation (UVPD) has been mainly investigated for the analysis of peptides and lipids while only in a limited way for LMWC. A triple quadrupole linear ion trap instrument has been modified to allow ultraviolet photodissociation (UVPD) in the end of the q2 region enabling various workflows with and without data-dependent acquisition (DDA) combining CID and UVPD in the same LC-MS analysis. The performance of UVPD, with a 266-nm laser, is compared to CID for a mix of 90 molecules from different classes of LMWC including peptides, pesticides, pharmaceuticals, metabolites, and drugs of abuse. These two activation methods offer complementary fragments as well as common fragments with similar sensitivities for most analytes investigated. The versatility of UVPD and CID is also demonstrated for quantitative analysis in human plasma of bosentan and its desmethyl metabolite, used as model analytes. Different background signals are observed for both fragmentation methods as well as unique fragments which opens the possibility of developing a selective quantitative assay with improved sample throughput, in particular for analytes present in different matrices.

Exploring the vacuum ultraviolet photochemistry of astrochemically important triatomic molecules.

The recently constructed vacuum ultraviolet (VUV) free electron laser (FEL) at the Dalian Coherent Light Source (DCLS) is yielding a wealth of new and exquisitely detailed information about the photofragmentation dynamics of many small gas-phase molecules. This Review focuses particular attention on five triatomic molecules-H2O, H2S, CO2, OCS and CS2. Each shows excitation wavelength-dependent dissociation dynamics, yielding photofragments that populate a range of electronic and (in the case of diatomic fragments) vibrational and rotational quantum states, which can be characterized by different translational spectroscopy methods. The photodissociation of an isolated molecule from a well-defined initial quantum state provides a lens through which one can investigate how and why chemical reactions occur, and provides numerous opportunities for fruitful, synergistic collaborations with high-level ab initio quantum chemists. The chosen molecules, their photofragments and the subsequent chemical reaction networks to which they can contribute are all crucial in planetary atmospheres and in interstellar and circumstellar environments. The aims of this Review are 3-fold: to highlight new photochemical insights enabled by the VUV-FEL at the DCLS, notably the recently recognized central atom elimination process that is shown to contribute in all of these triatomic molecules; to highlight some of the potential implications of this rich photochemistry to our understanding of interstellar chemistry and molecular evolution within the universe; and to highlight other and future research directions in areas related to chemical reaction dynamics and astrochemistry that will be enabled by increased access to VUV-FEL sources.

Photocaging of Carboxylic Function Bearing Biomolecules by New Thiazole Derived Fluorophore.

The design and synthesis of a new fluorophore containing an arylidene thiazole scaffold resulted in a compound with good photophysical characteristics. Furthermore, the thiazole C5-methyl group was easily modified into specific functional groups (CH2 Br and CH2 OH) for the formation of a series of photocourier molecules containing model compounds (benzoic acids), as well as prodrugs, including salicylic acid, caffeic acid, and chlorambucil via a "benzyl" linker. Spectral characteristics (1 H, 13 C NMR, and high-resolution mass spectra) corresponded to the proposed structures. The photocourier molecules demonstrated absorption with high values of coefficient of molar extinction, exhibited contrasting green emission, and showed good dark stability. The mechanism of the photorelease was investigated through spectral analysis, HPLC-HRMS, and supported by TD-DFT calculations. The photoheterolysis and elimination of carboxylic acids were proved to occur in the excited state, yielding a carbocation as an intermediate moiety. The fluorophore structure provided stability to the carbocation through the delocalization of the positive charge via resonance structures. Viability assessment of Vero cells using the MTT-test confirmed the weak cytotoxicity of prodrugs without irradiation and it increase upon UV-light.

Design Optimization of a Phototherapy Extracorporeal Membrane Oxygenator for Treating Carbon Monoxide Poisoning.

We designed a photo-ECMO device to speed up the rate of carbon monoxide (CO) removal by using visible light to dissociate CO from hemoglobin (Hb). Using computational fluid dynamics, fillets of different radii (5 cm and 10 cm) were applied to the square shape of a photo-ECMO device to reduce stagnant blood flow regions and increase the treated blood volume while being constrained by full light penetration. The blood flow at different flow rates and the thermal load imposed by forty external light sources at 623 nm were modeled using the Navier-Stokes and convection-diffusion equations. The particle residence times were also analyzed to determine the time the blood remained in the device. There was a reduction in the blood flow stagnation as the fillet radii increased. The maximum temperature change for all the geometries was below 4 °C. The optimized device with a fillet radius of 5 cm and a blood priming volume of up to 208 cm3 should decrease the time needed to treat CO poisoning without exceeding the critical threshold for protein denaturation. This technology has the potential to decrease the time for CO removal when treating patients with CO poisoning and pulmonary gas exchange inhibition.

Differentiation of free d-amino acids and amino acid isomers in solution using tandem mass spectrometry of hydrogen-bonded clusters.

Free d-amino acids and amino acid isomers were differentiated using tandem mass spectrometry without chromatographic separation. Ultraviolet photodissociation and water adsorption of leucine (Leu) and isoleucine (Ile) enantiomers hydrogen-bonded with tryptophan (Trp) were investigated at 8 K in the gas phase. The enantiomer-selective Cα-Cß bond cleavage of Trp was observed in the product ion spectra obtained by 285 nm photoexcitation, where the abundance of NH2CHCOOH-eliminated ion of heterochiral H+(d-Trp)(l-Leu) was higher than that of homochiral H+(l-Trp)(l-Leu). When comparing water adsorption on the surfaces of the heterochiral and homochiral clusters in a cold ion trap, the number of water molecules adsorbed on the heterochiral cluster was greater than that adsorbed on the homochiral cluster. These results indicate that the stronger intermolecular interactions within the homochiral H+(l-Trp)(l-Leu) compared to the heterochiral cluster inhibit enantiomer-selective photodissociation. Leu and Ile were differentiated by the isomer-selective Cα-Cß bond cleavage of Trp in the clusters. Calibration curves for the differentiation of isomeric amino acids and their enantiomers were developed using monitoring isomer- and enantiomer-selective photodissociation, indicating that the molar fractions in solution could be determined from a single product ion spectrum.

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies.

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.

Direct mass spectrometric imaging of document handwriting with laser desorption ionization and post ultraviolet photodissociation.

Handwriting represents personal education and physical or psychological states. This work describes a chemical imaging technique for document evaluation that combines laser desorption ionization with post ultraviolet photo-induced dissociation (LDI-UVPD) in mass spectrometry. Taken the advantages of chromophores in ink dyes, handwriting papers were subjected to direct laser desorption ionization without additional matrix materials. It is a surface-sensitive analytical method that uses a low intensity pulsed laser at 355 nm to remove chemical components from very outermost surfaces of overlapped handwritings. Meanwhile, the transfer of photoelectrons to those compounds leads to the ionization and the formation of radical anions. The gentle evaporation and ionization property enable the dissection of chronological orders. Paper documents maintain intact without extensive damages after laser irradiation. The evolving plume resulting from the irradiation of the 355 nm laser is fired by the second ultraviolet laser at 266 nm that is in parallel to the sample surface. In contrast to collision activated dissociation in tandem MS/MS, such post ultraviolet photodissociation generates much more different fragment ions through electron-directed specific cleavages of chemical bonds. LDI-UVPD can not only provide graphic representation of chemical components but also reveal hidden dynamic features such as alterations, pressures and aging.