Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF.

Endogenous antibodies, or immunoglobulins (Igs), abundantly present in body fluids, represent some of the most challenging samples to analyze, largely due to the immense variability in their sequences and concentrations. It has been estimated that our body can produce billions of different Ig proteins with different isotypes, making their individual analysis seemingly impossible. However, recent advances in protein-centric proteomics using LC-MS coupled to Orbitrap mass analyzers to profile intact Fab fragments formed by selective cleavage at the IgG-hinge revealed that IgG repertoires may be less diverse, albeit unique for each donor.

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 (/)-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 litmus test for the balanced description of dispersion interactions and coordination chemistry of lanthanoids.

The influence of long-range interactions on the structure of complexes of Eu(III) with four 9-hydroxy-phenalen-1-one ligands (HPLN) and one alkaline earth metal dication [Eu(PLN)AE] (AE: Mg, Ca, Sr, and Ba) is analyzed. Through the [Eu(PLN)Ca] complex, which is a charged complex with two metals-one of them a lanthanoid-and with four relatively fluxional π-ligands, the difficulties of describing such systems are identified. The inclusion of the D3(BJ) or D4 corrections to different density functionals introduces significant changes in the structure, which are shown to stem from the interaction between pairs of PLN ligands.

Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions.

Native top-down mass spectrometry (MS) is gaining traction for the analysis and sequencing of intact proteins and protein assemblies, giving access to their mass and composition, as well as sequence information useful for identification. Herein, we extend and apply native top-down MS, using electron capture dissociation, to two submillion Da IgM- and IgG-based oligomeric immunoglobulins. Despite structural similarities, these two systems are quite different.

Human plasma IgG1 repertoires are simple, unique, and dynamic.

Although humans can produce billions of IgG1 variants through recombination and hypermutation, the diversity of IgG1 clones circulating in human blood plasma has largely eluded direct characterization. Here, we combined several mass-spectrometry-based approaches to reveal that the circulating IgG1 repertoire in human plasma is dominated by a limited number of clones in healthy donors and septic patients. We observe that each individual donor exhibits a unique serological IgG1 repertoire, which remains stable over time but can adapt rapidly to changes in physiology.

Generating Informative Sequence Tags from Antigen-Binding Regions of Heavily Glycosylated IgA1 Antibodies by Native Top-Down Electron Capture Dissociation.

Immunoglobulins A (IgA) include some of the most abundant human antibodies and play an important role in defending mucosal surfaces against pathogens. The unique structural features of the heavy chain of IgA subclasses (called IgA1 and IgA2) enable them to polymerize via the joining J-chain, resulting in IgA dimers but also higher oligomers. While secretory sIgA oligomers are dominant in milk and saliva, IgAs exist primarily as monomers in serum.

Selectivity over coverage in sequencing of IgGs.

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies . Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous.

Enhancing Top-Down Analysis Using Chromophore-Assisted Infrared Multiphoton Dissociation from (Phospho)peptides to Protein Assemblies.

Infrared multiphoton dissociation (IRMPD) has been used in mass spectrometry to fragment peptides and proteins, providing fragments mostly similar to collisional activation. Using the 10.6 μm wavelength of a CO laser, IRMPD suffers from the relative low absorption cross-section of peptides and small proteins.

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry.

Ion mobility separates molecules in the gas-phase based on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, collision cell and a TOF mass analyzer, to probe ions at high speeds with on-the-fly fragmentation. Here, we show that on this platform ion mobility is beneficial for cross-linking MS (XL-MS).

Expanding the mass range for UVPD-based native top-down mass spectrometry.

Native top-down mass spectrometry is emerging as a methodology that can be used to structurally investigate protein assemblies. To extend the possibilities of native top-down mass spectrometry to larger and more heterogeneous biomolecular assemblies, advances in both the mass analyzer and applied fragmentation techniques are still essential. Here, we explore ultraviolet photodissociation (UVPD) of protein assemblies on an Orbitrap with extended mass range, expanding its usage to large and heterogeneous macromolecular complexes, reaching masses above 1 million Da.

Gas-Phase Photoluminescence and Photodissociation of Silver-Capped Hexagold Clusters.

We report on the radiative and nonradiative deactivation pathways of selected charge states of the stoichiometric hexagold phosphine-stabilized ionic clusters, [(C)(AuDppy)Ag·(BF) ] with x = 2 and 3 (Dppy = diphenylphosphino-2-pyridine), combining gas-phase photoluminescence and photodissociation with quantum chemical computations. These clusters possess an identical isostructural core made of a hyper-coordinated carbon at their center octahedrally surrounded by six gold ions, and two silver ions at their apexes. Their luminescence and fragmentation behavior upon photoexcitation was investigated under mass and charge control in an ion trap.

Vibronic Coupling Analysis of the Ligand-Centered Phosphorescence of Gas-Phase Gd(III) and Lu(III) 9-Oxophenalen-1-one Complexes.

The gas-phase laser-induced photoluminescence of cationic mononuclear gadolinium and lutetium complexes involving two 9-oxophenalen-1-one ligands is reported. Performing measurements at a temperature of 83 K enables us to resolve vibronic transitions. Via comparison to Franck-Condon computations, the main vibrational contributions to the ligand-centered phosphorescence are determined to involve rocking, wagging, and stretching of the 9-oxophenalen-1-one-lanthanoid coordination in the low-energy range, intraligand bending, and stretching in the medium- to high-energy range, rocking of the carbonyl and methine groups, and C-H stretching beyond.

Flyscan opportunities in medicine: the case of quantum rattle based on gold quantum dots.

The new rapid scan method, Flyscan mode, implemented on the DiffAbs beamline at Synchrotron SOLEIL, allows fast micro-X-ray fluorescence data acquisition. It paves the way for applications in the biomedical field where a large amount of data is needed to generate meaningful information for the clinician. This study presents a complete set of data acquired after injection of gold-cluster-enriched mesoporous silica nanospheres, used as potential theranostic vectors, into rats.

Correlation of the structural information obtained for europium-chelate ensembles from gas-phase photoluminescence and ion-mobility spectroscopy with density-functional computations and ligand-field theory.

We report a combined investigation of europium(iii)9-oxo-phenalen-1-one (PLN) coordination complexes, [Eu(PLN)AE] with AE = Mg, Ca, and Sr, using gas-phase photoluminescence, trapped ion-mobility spectrometry and density-functional computations. In order to sort out the structural impact of the alkali earth dications on the photoluminescence spectra, the experimental data are compared to the predicted ligand-field splittings as well as to the collision cross-sections for different isomers of [Eu(PLN)AE]. The best fitting interpretation is that one isomer family predominantly contributes to the recorded luminescence.

From Planar to Cage in 15 Easy Steps: Resolving the C60H21F9(-) → C60(-) Transformation by Ion Mobility Mass Spectrometry.

A combination of mass spectrometry, collision-induced dissociation, ion mobility mass spectrometry (IM-MS), and density functional theory (DFT) has been used to study the evolution of anionic species generated by laser-desorption of the near-planar, fluorinated polycyclic aromatic hydrocarbon (PAH), C60H21F9 (s). The dominant decay process for isolated, thermally activated C60H21F9(-) species comprises a sequence of multiple regioselective cyclodehydrofluorination and cyclodehydrogenation reactions (eliminating HF and H2, respectively, while forming additional pentagons and/or hexagons). The DFT calculations allow us to set narrow bounds on the structures of the resulting fragment ions by fitting structural models to experimentally determined collision cross sections.

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs.

Gas-Phase Photoluminescence Characterization of Stoichiometrically Pure Nonanuclear Lanthanoid Hydroxo Complexes Comprising Europium or Gadolinium.

Gas-phase photoluminescence measurements involving mass-spectrometric techniques enable determination of the properties of selected molecular systems with knowledge of their exact composition and unaffected by matrix effects such as solvent interactions or crystal packing. The resulting reduced complexity facilitates a comparison with theory. Herein, we provide a detailed report of the intrinsic luminescence properties of nonanuclear europium(III) and gadolinium(III) 9-hydroxyphenalen-1-one (HPLN) hydroxo complexes.

Photoluminescence Spectroscopy of Mass-Selected Electrosprayed Ions Embedded in Cryogenic Rare-Gas Matrixes.

An apparatus is presented which combines nanoelectrospray ionization for isolation of large molecular ions from solution, mass-to-charge ratio selection in gas-phase, low-energy-ion-beam deposition into a (co-condensed) inert gas matrix and UV laser-induced visible-region photoluminescence (PL) of the matrix isolated ions. Performance is tested by depositing three different types of lanthanoid diketonate cations including also a dissociation product species not directly accessible by chemical synthesis. For these strongly photoluminescent ions, accumulation of some femto- to picomoles in a neon matrix (over a time scale of tens of minutes to several hours) is sufficient to obtain well-resolved dispersed emission spectra.

Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase.

Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus.

Characterization of Nonanuclear Europium and Gadolinium Complexes by Gas-Phase Luminescence Spectroscopy.

Gas-phase measurements using mass-spectrometric techniques allow determination of the luminescence properties of selected molecular systems with knowledge of their exact composition. Furthermore, isolated luminophores are unaffected by matrix effects like solvent interactions or crystal packing. As a result, the system complexity is reduced relative to the condensed phase and a direct comparison with theory is facilitated.

Effect of Proton Substitution by Alkali Ions on the Fluorescence Emission of Rhodamine B Cations in the Gas Phase.

The photophysics of chromophores is strongly influenced by their environment. Solvation, charge state, and adduct formation significantly affect ground and excited state energetics and dynamics. The present study reports on fluorescence emission of rhodamine B cations (RhBH) and derivatives in the gas phase.

Substitutional photoluminescence modulation in adducts of a europium chelate with a range of alkali metal cations: a gas-phase study.

We present gas-phase dispersed photoluminescence spectra of europium(III) 9-hydroxyphenalen-1-one (HPLN) complexes forming adducts with alkali metal ions ([Eu(PLN)3M](+) with M = Li, Na, K, Rb, and Cs) confined in a quadrupole ion trap for study. The mass selected alkali metal cation adducts display a split hypersensitive (5)D0 → (7)F2 Eu(3+) emission band. One of the two emission components shows a linear dependence on the radius of the alkali metal cation whereas the other component displays a quadratic dependence thereon.

Intrinsic fluorescence properties of rhodamine cations in gas-phase: triplet lifetimes and dispersed fluorescence spectra.

We have investigated the gas phase triplet state lifetimes and dispersed fluorescence spectra of several types of rhodamine cations confined in a quadrupole ion trap and thermalized to 85 K. The measured triplet lifetimes of rhodamine cations Rh6G(+), Rh575(+), RhB(+), and Rh101(+) are found to be on the order of seconds, several orders of magnitude longer than those typically observed for the same dyes in optical condensed phase measurements. In addition dispersed fluorescence emission spectra in the gas phase at 85 K have been measured.

Gas phase fullerene anions hydrogenation by methanol followed by IRMPA dehydrogenation.

The characterization in the gas phase of the mechanisms responsible for hydride formation can contribute to the development of new materials for hydrogen storage. The present work provides evidence of a hydrogenation-dehydrogenation catalytic cycle for C(60)(*-) anions in the gas phase using methanol vapor at room temperature as hydrogen donor. The involvement of methanol in the reaction is confirmed by experiments using CD(3)OD and CD(3)OH.

Mass spectrometric study of the ionized C60: (gamma-Cyclodextrin)2 inclusion complex by collision induced dissociation.

The water soluble inclusion complex [C(60):(gamma-cyclodextrin)(2)] has been characterized using electrospray tandem mass spectrometry and collision induced dissociation. [C(60):(gamma-cyclodextrin)(2)] ions were detected in the gas phase as doubly deprotonated, doubly protonated and doubly sodiated ions. The absence of monocharged complex ions following electronebulization is a likely consequence of the dimeric nature and structural symmetry of the inclusion complex.