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. Serum repertoires seem to be dominated by a few hundred clones that cumulatively make up 50-95% of the total IgG content. Enabling such analyses required careful optimization of the chromatography and mass analysis, as all Fab analytes are highly alike in mass (46-51 kDa) and sequence. To extend the opportunities of this mass-spectrometry-based profiling of antibody repertoires, we here report the optimization and evaluation of an alternative MS platform, namely, the timsTOF, for antibody repertoire profiling. The timsTOF mass analyzer has gained traction in recent years for peptide-centric proteomics and found wide applicability in plasma proteomics, affinity proteomics, and HLA peptidomics, to name a few. However, for protein-centric analysis, this platform has been less explored. Here, we demonstrate that the timsTOF platform can be adapted to perform protein-centric LC-MS-based profiling of antibody repertoires. In a side-by-side comparison of the timsTOF and the Orbitrap we demonstrate that the extracted serum antibody repertoires are alike qualitatively and quantitatively, whereby in particular the sensitivity of the timsTOF platform excels. Future incorporation of advanced top-down capabilities on the timsTOF may make this platform a very valuable alternative for protein-centric proteomics and top-down proteomics and thus also for personalized antibody repertoire profiling.

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.

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)4AE]+ (AE: Mg, Ca, Sr, and Ba) is analyzed. Through the [Eu(PLN)4Ca]+ 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. This interaction is studied further with a variety of density functionals, wave-function based methods, and by means of the random phase approximation. By comparing the computed results with those from experimental evidence of gas-phase photoluminescence and ion mobility measurements it is concluded that the inclusion of dispersion corrections does not always yield structures that are in agreement with the experimental findings.

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. The ∼895 kDa noncovalent IgG hexamer consists of six IgG subunits hexamerizing in solution due to three specifically engineered mutations in the Fc region, whereas the ∼935 kDa IgM oligomer results from the covalent assembly of one joining (J) chain and 5 IgM subunits into an asymmetric "pentamer" stabilized by interchain disulfide bridges. Notwithstanding their size, structural differences, and complexity, we observe that their top-down electron capture dissociation spectra are quite similar and straightforward to interpret, specifically providing informative sequence tags covering the highly variable CDR3s and FR4s of the Ig subunits they contain. Moreover, we show that the electron capture dissociation fragmentation spectra of immunoglobulin oligomers are essentially identical to those obtained for their respective monomers. Demonstrated for recombinantly produced systems, the approach described here opens up new prospects for the characterization and identification of IgMs circulating in plasma, which is important since IgMs play a critical role in the early immune response to pathogens such as viruses and bacteria.

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. We introduce an integrative protein- and peptide-centric approach to obtain and validate a full sequence of an individual plasma IgG1 clone de novo. This IgG1 clone emerged at the onset of a septic episode and exhibited a high mutation rate (13%) compared with the closest matching germline DNA sequence, highlighting the importance of de novo sequencing at the protein level. A record of this paper's transparent peer review process is included in the supplemental information.

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. No method currently allows disentangling the millions of unique IgAs potentially present in the human antibody repertoire. Obtaining unambiguous sequence reads of their hypervariable antigen-binding regions is a prerequisite for IgA identification. We here report a mass spectrometric method that uses electron capture dissociation (ECD) to produce straightforward-to-read sequence ladders of the variable parts of both the light and heavy chains of IgA1s, in particular, of the functionally critical CDR3 regions. We directly compare the native top-down ECD spectra of a heavily and heterogeneously N- and O-glycosylated anti-CD20 IgA1, the corresponding N-glycosylated anti-CD20 IgG1, and their Fab parts. We show that while featuring very different MS1 spectra, the native top-down ECD MS2 spectra of all four species are nearly identical, with cleavages occurring specifically within the CDR3 and FR4 regions of both the heavy and light chain. From the sequence-informative ECD data of an intact glycosylated IgA1, we foresee that native top-down ECD will become a valuable complementary tool for the de novo sequencing of IgA1s from milk, saliva, or serum.

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 CO2 laser, IRMPD suffers from the relative low absorption cross-section of peptides and small proteins. Focusing on top-down analysis, we investigate different means to tackle this issue. We first reassess efficient sorting of phosphopeptides from nonphosphopeptides based on IR-absorption cross-sectional enhancement by phosphate moieties. We subsequently demonstrate that a myo-inositol hexakisphosphate (IP6) noncovalent adduct can substantially enhance IRMPD for nonphosphopeptides and that this strategy can be extended to proteins. As a natural next step, we show that native phospho-proteoforms of proteins display a distinct and enhanced fragmentation, compared to their unmodified counterparts, facilitating phospho-group site localization. We then evaluate the impact of size on the IRMPD of proteins and their complexes. When applied to protein complexes ranging from a 365 kDa CRISPR-Cas Csy ribonucleoprotein hetero-decamer, a 800 kDa GroEL homo-tetradecamer in its apo-form or loaded with its ATP cofactor, to a 1 MDa capsid-like homo-hexacontamer, we conclude that while phosphate moieties present in crRNA and ATP molecules enhance IRMPD, an increase in the IR cross-section with the size of the protein assembly also favorably accrues dissociation yields. Overall, our work showcases the versatility of IRMPD in the top-down analysis of peptides, phosphopeptides, proteins, phosphoproteins, ribonucleoprotein assemblies, and large protein complexes.

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). Cross-linking reagents covalently link amino acids in proximity, resulting in peptide pairs after proteolytic digestion. These cross-linked peptides are typically present at low abundance in the background of normal peptides, which can partially be resolved by using enrichable cross-linking reagents. Even with a very efficient enrichable cross-linking reagent, like PhoX, the analysis of cross-linked peptides is still hampered by the co-enrichment of peptides connected to a partially hydrolyzed reagent - termed mono-linked peptides. For experiments aiming to uncover protein-protein interactions these are unwanted byproducts. Here, we demonstrate that gas-phase separation by ion mobility enables the separation of mono-linked peptides from cross-linked peptide pairs. A clear partition between these two classes is observed at a CCS of 500 Å2 and a monoisotopic mass of 2 kDa, which can be used for targeted precursor selection. A total of 50-70% of the mono-linked peptides are prevented from sequencing, allowing the analysis to focus on sequencing the relevant cross-linked peptide pairs. In applications to both simple proteins and protein mixtures and a complete highly complex lysate this approach provides a substantial increase in detected cross-linked peptides.

Selectivity over coverage in de novo 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 de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab')2 part from the conserved Fc part, whereafter the F(ab')2 portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab')2 or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.

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. We demonstrate that UVPD can lead not only to the ejection of intact subunits directly from such large intact complexes, but also to backbone fragmentation of these subunits, providing enough sequence information for subunit identification. The Orbitrap mass analyzer enables simultaneous monitoring of the precursor, the subunits, and the subunit fragments formed upon UVPD activation. While only partial sequence coverage of the subunits is observed, the UVPD data yields information about the localization of chromophores covalently attached to the subunits of the light harvesting complex B-phycoerythrin, extensive backbone fragmentation in a subunit of a CRISPR-Cas Csy (type I-F Cascade) complex, and sequence modifications in a virus-like proteinaceous nano-container. Through these multiple applications we demonstrate for the first time that UVPD based native top-down mass spectrometry is feasible for large and heterogeneous particles, including ribonucleoprotein complexes and MDa virus-like particles.

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)6Ag2·(BF4) x](4- x)+ 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. The experimental and computational results shed light on the electronic states involved in the optical transitions as well as on their core, ligand, or charge transfer character. Gas-phase results are discussed in relation with condensed phase measurements, as well as previous observations in solution and on metal-organic frameworks. The monocationic species ( x = 3) is found to be less stable than the dicationic one ( x = 2). In the luminescence spectrum of the monocationic species, a shoulder at short wavelength can be observed and is assigned to fragment emission. This fragment formation appears to be favored for the monocation by the existence of a low lying singlet state energetically overlapping with the triplet state manifold, which is populated quickly after photoexcitation.

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. Whereas Franck-Condon calculations based on density-functional harmonic frequency computations reproduce the main features of the vibrationally resolved emission spectra, the absolute transition energies as determined by density functional theory are off by several thousand wavenumbers. This discrepancy is found to remain at higher computational levels. The relative energy of the Gd(III) and Lu(III) emission bands is only reproduced at the coupled-cluster singles and doubles level and 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. While classical X-ray fluorescence investigations (using step-by-step acquisitions) are based on a limited number of samples (approximately one per day at the DiffAbs beamline), the Flyscan mode has enabled gathering information on the interaction of nanometer-scale vectors in different organs such as liver, spleen and kidney at the micrometer scale, for five rats, in only a single five-day synchrotron shift. Moreover, numerous X-ray absorption near-edge structure spectra, which are beam-time-consuming taking into account the low concentration of these theranostic vectors, were collected.

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)4AE]+ 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)4AE]+. The best fitting interpretation is that one isomer family predominantly contributes to the recorded luminescence. The present work demonstrates the complexity of the coordination patterns of multicenter lanthanoid chelates involved in dynamical equilibria and the pertinence of using isolation techniques to elucidate their photophysical properties.

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. These show that the transformation of the precursor anion proceeds via a series of intermediate structures characterized by increasing curvature, ultimately leading to the closed-shell fullerene cage C60(-) as preprogrammed by the precursor structure.

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. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology.

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. Luminescence spectra of [Eu9(PLN)16(OH)10](+) ions reveal an europium-centered emission dominated by a 4-fold split Eu(III) hypersensitive transition, while photoluminescence lifetime measurements for both complexes support an efficient europium sensitization via a PLN-centered triplet-state manifold. The combination of gas-phase measurements with density functional theory computations and ligand-field theory is used to discuss the antiprismatic core structure of the complexes and to shed light on the energy-transfer mechanism. This methodology is also employed to fit a new set of parameters, which improves the accuracy of ligand-field computations of Eu(III) electronic transitions for gas-phase species.

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. We have ruled out contributions to these spectra due to charge neutralization or fragmentation during deposition by also acquiring photoluminescence spectra of the same ionic species in the gas phase.

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. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.

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. Substitution of the acidic proton of RhBH+ by alkali metal cations, M+, ranging from lithium to cesium leads to significant and systematic blue shifts of the emission. The gas-phase structures and singlet transition energies of RhBH+ and RhBM+, M = Li, Na, K, Rb, and Cs, were investigated using Hartree-Fock theory, density functional methods, second-order Møller-Plesset perturbation theory, and the second-order approximate coupled-cluster model CC2. Comparison of experimental and theoretical results highlights the need for improved quantum chemical methods, while the hypsochromic shift observed upon substitution appears best explained by the Stark effect due to the inhomogeneous electric field generated by the alkali ions.