Single Cell Analysis of Proteoforms.

We introduce single cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.

Precise Readout of MEK1 Proteoforms upon MAPK Pathway Modulation by Individual Ion Mass Spectrometry.

The functions of proteins bearing multiple post-translational modifications (PTMs) are modulated by their modification patterns, yet precise characterization of them is difficult. MEK1 (also known as MAP2K1) is one such example that acts as a gatekeeper of the mitogen-activating protein kinase (MAPK) pathway and propagates signals via phosphorylation by upstream kinases. In principle, top-down mass spectrometry can precisely characterize whole MEK1 proteoforms, but fragmentation methods that would enable the site-specific characterization of labile modifications on 43 kDa protein ions result in overly dense tandem mass spectra. By using the charge-detection method called individual ion mass spectrometry, we demonstrate how complex mixtures of phosphoproteoforms and their fragment ions can be reproducibly handled to provide a "bird's eye" view of signaling activity through mapping proteoform landscapes in a pathway. Using this approach, the overall stoichiometry and distribution of 0-4 phosphorylations on MEK1 was determined in a cellular model of drug-resistant metastatic melanoma. This approach can be generalized to other multiply modified proteoforms, for which PTM combinations are key to their function and drug action.

Decoding the protein composition of whole nucleosomes with Nuc-MS.

Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the 'histone code'. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology.

Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes.

Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.

Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes.

An Orbitrap-based ion analysis procedure determines the direct charge for numerous individual protein ions to generate true mass spectra. This individual ion mass spectrometry (I2MS) method for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by typical measurements of ensembles of ions.

Electronic Structure of Heteronuclear Cerium-Platinum Clusters.

Beyond the now well-known strong catalyst-support interactions reported for ceria-supported platinum catalysts, intermetallic Ce-Pt compounds exhibit fascinating properties such as heavy fermion behavior and magnetic instability. Small heterometallic Ce-Pt clusters, which can provide insights into the local features that govern bulk phenomena, have been less explored. Herein, the anion photoelectron spectra of three small mixed Ce-Pt clusters, Ce2OPt-, Ce2Pt-, and Ce3Pt-, are presented and interpreted with supporting density functional theory calculations. The calculations, which are readily reconciled with the experimental spectra, suggest the presence of numerous close-lying spin states, including states in which the Ce 4f electrons are ferromagnetically coupled or antiferromagnetically coupled. The Pt center is consistently in a nominal -2 charge state in all cluster neutrals and anions, giving the Ce-Pt bond ionic character. Ce-Pt bonds are stronger than Ce-Ce bonds, and the O atom in Ce2OPt- coordinates only with the Ce centers. The energy of the singly occupied Ce-local 4f orbitals relative to the Pt-local orbitals changes with cluster composition. Discussion of the results includes potential implications for Ce-rich intermetallic materials.

Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS.

SARS-CoV-2 Omicron (B.1.1.529) and its subvariants are currently the most common variants of concern worldwide, featuring numerous mutations in the spike protein and elsewhere that collectively make Omicron variants more transmissible and more resistant to antibody-mediated neutralization provided by vaccination, previous infections, and monoclonal antibody therapies than their predecessors. We recently reported the creation and characterization of Ig-MS, a new mass spectrometry-based serology platform that can define the repertoire of antibodies against an antigen of interest at single proteoform resolution. Here, we applied Ig-MS to investigate the evolution of plasma antibody repertoires against the receptor-binding domain (RBD) of SARS-CoV-2 in response to the booster shot and natural viral infection. We also assessed the capacity for antibody repertoires generated in response to vaccination and/or infection with the Omicron variant to bind to both Wuhan- and Omicron-RBDs. Our results show that (1) the booster increases antibody titers against both Wuhan- and Omicron- RBDs and elicits an Omicron-specific response and (2) vaccination and infection act synergistically in generating anti-RBD antibody repertoires able to bind both Wuhan- and Omicron-RBDs with variant-specific antibodies.

Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire.

Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS, a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multiparametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We applied Ig-MS to plasma from subjects with severe and mild COVID-19 and immunized subjects after two vaccine doses, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, that could use other antigens of interest to gauge immune responses to vaccination, pathogens, or autoimmune disorders.

Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra.

Charge detection mass spectrometry (CDMS) provides mass domain spectra of large and highly heterogeneous analytes. Over the past few years, we have multiplexed CDMS on Orbitrap instruments, an approach termed Individual Ion Mass Spectrometry (I2MS). Until now, I2MS required manual adjustment of injection times to collect spectra in the individual ion regime. To increase sample adaptability, enable online separations, and reduce the barrier for entry, we report an automated method for adjusting ion injection times in I2MS for image current detectors like the Orbitrap. Automatic Ion Control (AIC) utilizes the density of signals in the m/z domain to adjust an ensemble of ions down to the individual ion regime in real-time. The AIC technique was applied to both denatured and native proteins yielding high quality data without human intervention directly in the mass domain.

Isotopic Resolution of Protein Complexes up to 466 kDa Using Individual Ion Mass Spectrometry.

Native mass spectrometry involves transferring large biomolecular complexes into the gas phase, enabling the characterization of their composition and stoichiometry. However, the overlap in distributions created by residual solvation, ionic adducts, and post-translational modifications creates a high degree of complexity that typically goes unresolved at masses above ∼150 kDa. Therefore, native mass spectrometry would greatly benefit from higher resolution approaches for intact proteins and their complexes. By recording mass spectra of individual ions via charge detection mass spectrometry, we report isotopic resolution for pyruvate kinase (232 kDa) and ß-galactosidase (466 kDa), extending the limits of isotopic resolution for high mass and high m/z by >2.5-fold and >1.6-fold, respectively.

Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry.

Charge detection mass spectrometry (CDMS) is mainly utilized to determine the mass of intact molecules. Previous applications of CDMS have determined the mass-to-charge ratio and the charge of large polymers, DNA molecules, and native protein complexes, from which corresponding mass values could be assigned. Recent advances have demonstrated that CDMS using an Orbitrap mass analyzer yields the reliable assignment of integer charge states that enables individual ion mass spectrometry (I2MS) and spectral output directly into the mass domain. Here I2MS analysis was extended to isotopically resolved fragment ions from intact proteoforms for the first time. With a radically different bias for ion readout, I2MS identified low-abundance fragment ions containing many hundreds of residues that were undetectable by standard Orbitrap measurements, leading to a doubling in the sequence coverage of triosephosphate isomerase. Thus MS/MS with the detection of individual ions (MS/I2MS) provides a far greater ability to detect high mass fragment ions and exhibits strong complementarity to traditional spectral readout in this, its first application to top-down mass spectrometry.

Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins.

It is well-known that with Orbitrap-based Fourier-transform-mass-spectrometry (FT-MS) analysis, longer-time-domain signals are needed to better resolve species of interest. Unfortunately, increasing the signal-acquisition period comes at the expense of increasing ion decay, which lowers signal-to-noise ratios and ultimately limits resolution. This is especially problematic for intact proteins, including antibodies, which demonstrate rapid decay because of their larger collisional cross-sections, and result in more frequent collisions with background gas molecules. Provided here is a method that utilizes numerous low-ion-count spectra and single-ion processing to reconstruct a conventional m/ z spectrum. This technique has been applied to proteins varying in molecular weight from 8 to 150 kDa, with a resolving power of 677 000 achieved for transients of carbonic anhydrase (29 kDa) with a duration of only ∼250 ms. A resolution improvement ranging from 10- to 20-fold was observed for all proteins, providing isotopic resolution where none was previously present.

Molybdenum Oxide Cluster Anion Reactions with C2H4 and H2O: Cooperativity and Chemifragmentation.

To probe the mechanism of sacrificial reagents in catalytic processes, product distributions from MoxOy- clusters reacting individually with C2H4 and H2O are compared with those from reactions with a C2H4 + H2O mixture, with the thermodynamics explored computationally. These molecules were chosen to model production of H2 from H2O via H2O + C2H4 → H2 + CH3CHO, mediated by MoxOy- clusters. H2O is known to sequentially oxidize MoxOy- suboxide clusters while producing H2, resulting in less reactive clusters. MoxOy- (y ∼ x) clusters undergo chemi-fragmentation reactions with C2H4, with MoxOyC2Hz- complexes forming as the cluster oxidation state increases. Unique species observed in reactions with the C2H4 + H2O mixture, Mo2O5C2H2- and MoO3C2H4-, suggest that the internal energy gained in new Mo-O bond formation from oxidation by H2O opens additional reaction channels. C2H3O- is observed uniquely in reactions with the C2H4 + H2O mixture, giving indirect evidence of CH3CHO formation via the cluster mediated H2O + C2H4 → H2 + CH3CHO reaction; C2H3O- can form via dissociative electron attachment to CH3CHO. Calculations support mechanisms that invoke participation of two ethylene molecules on thermodynamically favorable pathways leading to experimentally observed products.

Exotic electronic structures of SmxCe3-xOy (x = 0-3; y = 2-4) clusters and the effect of high neutral density of low-lying states on photodetachment transition intensities.

Lanthanide (Ln) oxide clusters have complex electronic structures arising from the partially occupied Ln 4f subshell. New anion photoelectron (PE) spectra of SmxCe3-xOy- (x = 0-3; y = 2-4) along with supporting results of density functional theory (DFT) calculations suggest interesting x and y-dependent Sm 4f subshell occupancy with implications for Sm-doped ionic conductivity of ceria, as well as the overall electronic structure of the heterometallic oxides. Specifically, the Sm centers in the heterometallic species have higher 4f subshell occupancy than the homonuclear Sm3Oy-/Sm3Oy clusters. The higher 4f subshell occupancy both weakens Sm-O bonds and destabilizes the 4f subshell relative to the predominantly O 2p bonding orbitals in the clusters. Parallels between the electronic structures of these small cluster systems with bulk oxides are explored. In addition, unusual changes in the excited state transition intensities, similar to those observed previously in the PE spectra of Sm2O- and Sm2O2- [J. O. Kafader et al., J. Chem. Phys. 146, 194310 (2017)], are also observed in the relative intensities of electronic transitions to excited neutral state bands in the PE spectra of SmxCe3-xOy- (x = 1-3; y = 2, 4). The new spectra suggest that the effect is enhanced with lower oxidation states and with an increasing number of Sm atoms, implying that the prevalence of electrons in the diffuse Sm 6s-based molecular orbitals and a more populated 4f subshell both contribute to this phenomenon. Finally, this work identifies challenges associated with affordable DFT calculations in treating the complex electronic structures exhibited by these systems, including the need for a more explicit treatment of strong coupling between the neutral and PE.

Ce in the +4 oxidation state: Anion photoelectron spectroscopy and photodissociation of small CexOyHz- molecules.

The anion photoelectron (PE) spectra of a range of small mono-cerium molecular species, along with the Ce2O4- and Ce3O6- stoichiometric clusters, are presented and analyzed with the support of density functional theory calculations. A common attribute of all of the neutral species is that the Ce centers in both the molecules and clusters are in the +4 oxidation state. In bulk ceria (CeO2), an unoccupied, narrow 4f band lies between the conventional valence (predominantly O 2p) and conduction (Ce 5d) bands. Within the CeO2-, CeO3H2-, and Ce(OH)4- series, the PE spectra and computational results suggest that the Ce 6s-based molecular orbital is the singly occupied HOMO in CeO2- but becomes destabilized as the Ce 4f-local orbital becomes stabilized with increasing coordination. CeO3-, a hyperoxide, undergoes photodissociation with 3.49 eV photon energy to form the stoichiometric neutral CeO2 and O-. In the CeO2-, Ce2O4- ,and Ce3O6- stoichiometric cluster series, the 6s destabilization with 4f stabilization is associated with increasing cluster size, suggesting that a bulk-like band structure may be realized with fairly small cluster sizes. The destabilization of the 6s-based molecular orbitals can be rationalized by their diffuse size relative to Ce-O bond lengths in a crystal structure, suggesting that 6s bands in the bulk may be relegated to the surface.

The electron shuffle: Cerium influences samarium 4f orbital occupancy in heteronuclear Ce-Sm oxide clusters.

The anion photoelectron (PE) spectra along with supporting results of density functional theory (DFT) calculations on SmO-, SmCeOy-, and Sm2Oy- (y = 1, 2) are reported and compared to previous results on CeO- [M. Ray et al., J. Chem. Phys. 142, 064305 (2015)] and Ce2Oy- (y = 1, 2) [J. O. Kafader et al., J. Chem. Phys. 145, 154306 (2016)]. Similar to the results on CexOy- clusters, the PE spectra of SmO-, SmCeOy-, and Sm2Oy- (y = 1, 2) all exhibit electronic transitions to the neutral ground state at approximately 1 eV e-BE. The Sm centers in SmO and Sm2O2 neutrals can be described with the 4f56s superconfiguration, which is analogous to CeO and Ce2O2 neutrals in which the Ce centers can be described with the 4f 6s superconfiguration (ZCe = ZSm - 4). The Sm center in CeSmO2, in contrast, has a 4f6 occupancy, while the Ce center maintains the 4f 6s superconfiguration. The less oxidized Sm centers in both Sm2O and SmCeO have 4f6 6s occupancies. The 4f6 subshell occupancy results in relatively weak Sm-O bond strengths. If this extra 4f occupancy also occurs in bulk Sm-doped ceria, it may play a role in the enhanced O2- ionic conductivity in Sm-doped ceria. Based on the results of DFT calculations, the heteronuclear Ce-Sm oxides have molecular orbitals that are distinctly localized Sm 4f, Sm 6s, Ce 4f, and Ce 6s orbitals. The relative intensity of two electronic bands in the PE spectrum of Sm2O- exhibits an unusual photon energy-dependence, and the PE spectrum of Sm2O2- exhibits a photon energy-dependent continuum signal between two electronic transitions. Several explanations, including the high magnetic moment of these suboxide species and the presence of low-lying quasi-bound anion states, are considered.

Role of weakly bound complexes in temperature-dependence and relative rates of M(x)O(y)(-) + H2O (M = Mo, W) reactions.

Results of a systematic comparison of the MoxOy (-) + H2O and WxOy (-) + H2O reaction rate coefficients are reported and compared to previous experimental and computational studies on these reactions. WxOy (-) clusters undergo more direct oxidation by water to yield WxOy+1 (-) + H2, while for MoxOy (-) clusters, production of MoxOyH2 (-) (trapped intermediates in the oxidation reaction) is comparatively more prevalent. However, MoxOy (-) clusters generally have higher rate coefficients than analogous WxOy (-) clusters if MoxOy+1H2 (-) formation is included. Results of calculations on the M2Oy (-) + H2O (M = Mo, W; y = 4, 5) reaction entrance channel are reported. They include charge-dipole complexes formed from long-range interactions, and the requisite conversion to a Lewis acid-base complex that leads to MxOy+1H2 (-) formation. The results predict that the Lewis acid-base complex is more strongly bound for MoxOy (-) clusters than for WxOy (-) clusters. The calculated free energies along this portion of the reaction path are also consistent with the modest anti-Arrhenius temperature dependence measured for most MoxOy (-) + H2O reactions, and the WxOy (-) + H2O reaction rate coefficients generally being constant over the temperature range sampled in this study. For clusters that exhibit evidence of both water addition and oxidation reactions, increasing the temperature increases the branching ratio toward oxidation for both species. A more direct reaction path to H2 production may therefore become accessible at modest temperatures for certain cluster stoichiometries and structures.

Molecular and electronic structures of cerium and cerium suboxide clusters.

The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce-O-Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two-electron transitions possible in molecules with abundant nearly degenerate partially occupied orbitals.

Mixed cerium-platinum oxides: Electronic structure of [CeO]Ptn (n = 1, 2) and [CeO2]Pt complex anions and neutrals.

The electronic structures of several small Ce-Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt2 both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt2 complexes are therefore ionic, with electronic structures described qualitatively as [CeO(+2)]Pt(-2) and [CeO(+)]Pt2 (-), respectively. The associated anions are described qualitatively as [CeO(+)]Pt(-2) and [CeO(+)]Pt2 (-2), respectively. In both neutrals and anions, the most stable molecular structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt2 moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO2, which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO2]Pt(-). The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO2]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt-O-Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt(-) daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.

Photoelectron spectrum of PrO(-).

The photoelectron (PE) spectrum of PrO(-) exhibits a short 835 ± 20 cm(-1) vibrational progression of doublets (210 ± 30 cm(-1) splitting) assigned to transitions from the 4f(2) [(3)H4] σ6s (2) Ω = 4 anion ground state to the 4f(2) [(3)H4] σ6s Ω = 3.5 and 4.5 neutral states. This assignment is analogous to that of the recently reported PE spectrum of CeO(-), though the 82 cm(-1) splitting between the 4f [(2)F2.5] σ6s Ω = 2 and Ω = 3 CeO neutral states could not be resolved [Ray et al., J. Chem. Phys. 142, 064305 (2015)]. The origin of the transition to the Ω = 3.5 neutral ground state is 0.96 ± 0.01 eV, which is the adiabatic electron affinity of PrO. Density functional theory calculations on the anion and neutral molecules support the assignment. The appearance of multiple, irregularly spaced and low-intensity features observed ca. 1 eV above the ground state cannot be reconciled with low-lying electronic states of PrO that are accessible via one-electron detachment. However, neutral states correlated with the 4f(2) [(3)H4] 5d superconfiguration are predicted to be approximately 1 eV above the 4f(2) [(3)H4] σ6s Ω = 3.5 neutral ground state, leading to the assignment of these features to shake-up transitions to the excited neutral states. Based on tentative hot band transition assignments, the term energy of the previously unobserved 4f(2) [(3)H4] σ6s Ω = 2.5 neutral state is determined to be 1840 ± 110 cm(-1).