Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation.

Cyclosporin A (CycA) is a peptide secondary metabolite derived from fungi that plays a crucial role in transplantation surgery. Cyclic traveling wave ion mobility mass spectrometry (IM-MS) revealed an N → O peptidyl shift in singly protonated CycA to isocyclosporin A (isoA), whereas no such isomerization was observed for doubly protonated and sodiated molecules. CycA and isoA were able to be separated by considering doubly protonated precursors using a specific ion fragment. In parallel, sodium ion stabilization facilitated the simultaneous separation and quantitation of singly charged cyclosporin isomers with the limit of detection and coefficient of determination of 1.3% and 0.9908 for CycA in isoA and 1.0% and 0.9830 for isoA in CycA, respectively. Finally, 1H-13C gHSQC NMR experiments permitted parallel recording of up to 11 cyclosporin conformers. The ratios were determined by integrating the volume of cross-peaks of the upfield resonating hydrogen in the diastereotopic methylene group of sarcosine-3.

Experimental hierarchy of the nonclassicality of single-qubit states via potentials for entanglement, steering, and Bell nonlocality.

Entanglement potentials are a promising way to quantify the nonclassicality of single-mode states. They are defined by the amount of entanglement (expressed by, e.g., the Wootters concurrence) obtained after mixing the examined single-mode state with a purely classical state; such as the vacuum or a coherent state. We generalize the idea of entanglement potentials to other quantum correlations: the EPR steering and Bell nonlocality, thus enabling us to study mutual hierarchies of these nonclassicality potentials. Instead of the usual vacuum and one-photon superposition states, we experimentally test this concept using specially tailored polarization-encoded single-photon states. One polarization encodes a given nonclassical single-mode state, while the other serves as the vacuum place-holder. This technique proves to be experimentally more convenient in comparison to the vacuum and a one-photon superposition as it does not require the vacuum detection.

Nitrile Imines as Peptide and Oligonucleotide Photo-Cross-Linkers in Gas-Phase Ions.

Nitrile imines produced by photodissociation of 2,5-diaryltetrazoles undergo cross-linking reactions with amide groups in peptide-tetrazole (tet-peptide) conjugates and a tet-peptide-dinucleotide complex. Tetrazole photodissociation in gas-phase ions is efficient, achieving ca. 50% conversion with 2 laser pulses at 250 nm. The formation of cross-links was detected by CID-MS3 that showed structure-significant dissociations by loss of side-chain groups and internal peptide segments. The structure and composition of cross-linking products were established by a combination of UV-vis action spectroscopy and cyclic ion mobility mass spectrometry (c-IMS). The experimental absorption bands were found to match the bands calculated for vibronic absorption spectra of nitrile imines and cross-linked hydrazone isomers. The calculated collision cross sections (CCSth) for these ions were related to the matching experimental CCSexp from multipass c-IMS measurements. Loss of N2 from tet-peptide conjugates was calculated to be a mildly endothermic reaction with ΔH0 = 80 kJ mol-1 in the gas phase. The excess energy in the photolytically formed nitrile imine is thought to drive endothermic proton transfer, followed by exothermic cyclization to a sterically accessible peptide amide group. The exothermic nitrile imine reaction with peptide amides is promoted by proton transfer and may involve an initial [3 + 2] cycloaddition followed by cleavage of the oxadiazole intermediate. Nucleophilic groups, such as cysteine thiol, did not compete with the amide cyclization. Nitrile imine cross-linking to 2'-deoxycytidylguanosine was found to be >80% efficient and highly specific in targeting guanine. The further potential for exploring nitrile-imine cross-linking for biomolecular structure analysis is discussed.

Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study.

d(GCGAAGC) is the smallest oligonucleotide with a well-defined hairpin structure in solution. We report a study of multiply protonated d(GCGAAGC) and its sequence-scrambled isomers, d(CGAAGCG), d(GCGAACG), and d(CGGAAGC), that were produced by electrospray ionization with the goal of investigating their gas-phase structures and dissociations. Cyclic ion mobility measurements revealed that dications of d(GCGAAGC) as well as the scrambled-sequence ions were mixtures of protomers and/or conformers that had collision cross sections (CCS) within a 439-481 Å2 range. Multiple ion conformers were obtained by electrospray under native conditions as well as from aqueous methanol. Arrival time distribution profiles were characteristic of individual isomeric heptanucleotides. Extensive Born-Oppenheimer molecular dynamics (BOMD) and density functional theory (DFT) calculations of d(GCGAAGC)2+ isomers indicated that hairpin structures were high-energy isomers of more compact distorted conformers. Protonation caused a break up of the C2···G6 pair that was associated with the formation of strong hydrogen bonds in zwitterionic phosphate anion-nucleobase cation motifs that predominated in low energy ions. Multiple components were also obtained for d(GCGAAGC)3+ trications under native and denaturing electrospray conditions. The calculated trication structures showed disruption of the G···C pairs in low energy zwitterions. A hairpin trication was calculated to be a high energy isomer. d(GCGAAGC)4+ tetracations were produced and separated by c-IMS as two major isomers. All low energy d(GCGAAGC)4+ ions obtained by DFT geometry optimizations were zwitterions in which all five purine bases were protonated, and the ion charge was balanced by a phosphate anion. Tetracations of the scrambled sequences were each formed as one dominant isomer. The CCS calculated with the MobCal-MPI method were found to closely match experimental values. Collision-induced dissociation (CID) spectra of multiply charged heptanucleotides showed nucleobase loss and backbone cleavages occurring chiefly at the terminal nucleosides. Electron-transfer-CID tandem mass spectra were used to investigate dissociations of different charge and spin states of charge-reduced heptanucleotide cation radicals.

Synergic quantum generative machine learning.

We introduce a new approach towards generative quantum machine learning significantly reducing the number of hyperparameters and report on a proof-of-principle experiment demonstrating our approach. Our proposal depends on collaboration between the generators and discriminator, thus, we call it quantum synergic generative learning. We present numerical evidence that the synergic approach, in some cases, compares favorably to recently proposed quantum generative adversarial learning. In addition to the results obtained with quantum simulators, we also present experimental results obtained with an actual programmable quantum computer. We investigate how a quantum computer implementing generative learning algorithm could learn the concept of a maximally-entangled state. After completing the learning process, the network is able both to recognize and to generate an entangled state. Our approach can be treated as one possible preliminary step to understanding how the concept of quantum entanglement can be learned and demonstrated by a quantum computer.

Experimental hierarchy of two-qubit quantum correlations without state tomography.

A Werner state, which is the singlet Bell state affected by white noise, is a prototype example of states, which can reveal a hierarchy of quantum entanglement, steering, and Bell nonlocality by controlling the amount of noise. However, experimental demonstrations of this hierarchy in a sufficient and necessary way (i.e., by applying measures or universal witnesses of these quantum correlations) have been mainly based on full quantum state tomography, corresponding to measuring at least 15 real parameters of two-qubit states. Here we report an experimental demonstration of this hierarchy by measuring only six elements of a correlation matrix depending on linear combinations of two-qubit Stokes parameters. We show that our experimental setup can also reveal the hierarchy of these quantum correlations of generalized Werner states, which are any two-qubit pure states affected by white noise.

Separation of Isomeric Tau Phosphopeptides from Alzheimer's Disease Brain by Cyclic Ion Mobility Mass Spectrometry.

Alzheimer's disease (AD) is a neurodegenerative disorder of increasing concern. It belongs to diseases termed tauopathies which are characterized by inclusions of abnormally hyperphosphorylated and truncated forms of the protein tau. Studies of tauopathies often focus on detection and characterization of these aberrant tau proteoforms, in particular the phosphorylation sites, which represent a significant analytical challenge for example when several phosphosites can be present on the same peptide. Such isomers can even be difficult to fully separate chromatographically. Since recently introduced cyclic ion mobility-mass spectrometry can offer different selectivity, we have investigated the closely positioned phosphorylation sites S214, T212, and T217 of a tryptic peptide from proline rich region of tau-TPSLPTPPTREPK. The conformational heterogeneity of the isomeric peptides in the gas phase hindered their separation due to their overlapping arrival time distributions. Increasing the resolution of the analysis alone is insufficient to distinguish the peptides in a mixture typical of patient samples. We therefore developed a method based on a combination of collision-induced dissociation, isomeric product ions (m/z 677) mobility separation and post-mobility dissociation to aid in analyzing the isomeric phosphopeptides of tau in diseased brain extract. For all three isomers (T212, S214, and T217), the ion mobility signal of the ion at m/z 677 was still observable at the concentration of 0.1 nmol/L. This work not only offers insights into the phosphorylation of tau protein in AD but also provides an analytical workflow for the characterization of challenging pathological protein modifications in neurodegenerative diseases.

Detailed insight into chromium species released from failed CoCrMo implants: Ex vivo periprosthetic tissues study.

This unique study provides information on Cr species and their distribution in periprosthetic tissues of patients with metal-on-polyethylene joint implants. Co-Cr-Mo alloy has been widely used in joint replacement and represents a source of metal derived species. In the case of chromium, previous studies on periprosthetic tissues revealed mainly Cr(III) distribution, whereas the potential release of carcinogenic Cr(VI) species has been still a subject of debate. Here, an analytical approach utilizing speciation and fractionation was developed to analyze periprosthetic tissue samples collected from wide range of patients with failed total hip or knee replacements. The results reveal that Cr(III) is mainly released in the form of insoluble CrPO4 and Cr2 O3 particles. The highest Cr contents were found in periprosthetic tissues of patients suffering from aseptic loosening and having more Cr-based implants in the body. Cr species penetrated tissue layers, but their levels decreased with the distance from an implant. The detailed speciation/fractionation study carried out using the set of consecutive periprosthetic tissues of a patient with extensive metallosis showed the presence of trace amounts of free Cr(III), nanoparticles, and metal-protein complexes, but the majority of Cr still occurred in CrPO4 form. Carcinogenic Cr(VI) species were not detected. Up to date, there is no published human tissue study focused on the detailed speciation of both soluble and insoluble Cr-based species in the context of failing total hip and knee replacements.

Dual-polarity MALDI mass spectrometry and imaging of oil binders and fatty acids in artworks using cyanographene as a single matrix.

Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and imaging mass spectrometry (IMS) are being increasingly recognized for the detection and visualization of various organic species including lipids and fatty acids. Nevertheless, most MALDI matrices perform optimally in one ionization mode. This study investigates the performance of cyano derivative of graphene (G-CN) as a matrix in two polarities of MALDI MS and IMS for the detection of oil binders and fatty acids in artworks, and compares it with classical MALDI matrices (2,5-dihydroxybenzoic acid, 9-aminoacridine). Results revealed the ability of G-CN to provide high quality positive and negative mass spectra of oils and fatty acids, respectively, with lowest matrix-induced interferences among tested matrices and minimal effects of the presence of inorganic pigments. The newly developed approach makes both oil and fatty acid identifiable in a single spot simply by covering the sample surface with one matrix and switching the polarity in MALDI without any sample manipulation. G-CN offers effective matrix to analyte energy transfer, ability to detect components in less than 100 ng of oil at a MALDI spot and lesser analyte fragmentation than the compared conventional matrices. Furthermore, it enables direct mapping of specific m/z features corresponding to triacylglycerol (TAG), products of TAG oxidation and deprotonated acids using one nanoparticle matrix in MALDI IMS. This research shows potential for technical innovations in the study of art micro-environments and degradation phenomena of historical artworks.

Unified chromatography - Mass spectrometry as a versatile tool for determination of food dyes.

Unified chromatography with mass spectrometric detection was assessed for determination of food dyes. Nineteen substances representing azo, triphenylmethane, xanthone, indigoid, quinoline and polyene classes covering an unprecedented range from nonpolar ß-Carotene (logD 13.6) to ionic Tartrazine (logD -7.5) were analyzed simultaneously. The dyes were separated in a single experimental run by an 18-min gradient elution from 98% CO2 to 100% aqueous-methanolic modifier on a diol column. Isomeric substances were resolved, and Isatin Sulfonic acid was detected as a degradation product of Indigo Carmine. Mobile phase properties reproducibly changed from supercritical to liquid state ensuring stable retention times (inter-day RSD<0.5%). Quantitative analysis of sports drinks after straightforward 10- or 25-fold dilution with dimethyl sulfoxide confirmed the method applicability to real-life samples. Sufficient limits of detection (typically 0.025 mg L-1 in processed samples, equivalent to 0.25 mg L-1 in drink) and a wide linear range (typically 0.5-50 mg L-1 or 1.3-125 mg L-1 in drink for 10× or 25× dilution, respectively) were demonstrated during validation. A comparison of method performance with competitive liquid chromatography procedures is also provided. Unified chromatography is a promising tool for comprehensive multiclass analysis of dyes in the context of food safety.

Probing d- and l-Adrenaline Binding to ß2-Adrenoreceptor Peptide Motifs by Gas-Phase Photodissociation Cross-Linking and Ion Mobility Mass Spectrometry.

Diazirine-tagged d- and l-adrenaline derivatives formed abundant noncovalent gas-phase ion complexes with peptides N-Ac-SSIVSFY-NH2 (peptide S) and N-Ac-VYILLNWIGY-NH2 (peptide V) upon electrospray ionization. These peptide sequences represent the binding motifs in the ß2-adrenoreceptor. The structures of the gas-phase complexes were investigated by selective laser photodissociation of the diazirine chromophore at 354 nm, which resulted in a loss of N2 and formation of a transient carbene intermediate in the adrenaline ligand without causing its expulsion. The photolyzed complexes were analyzed by collision-induced dissociation (CID-MS3 and CID-MS4) in an attempt to detect cross-links and establish the binding sites. However, no cross-linking was detected in the complexes regardless of the peptide and d- or l-configuration in adrenaline. Cyclic ion mobility measurements were used to obtain collision cross sections (CCS) in N2 for the peptide S complexes. These showed identical values, 334 ± 0.9 Å2, for complexes of the l- and d-adrenaline derivatives, respectively. Identical CCS were also obtained for peptide S complexes with natural l- and d-adrenaline, 317 ± 1.2 Å2, respectively. Born-Oppenheimer molecular dynamics (BOMD) in combination with full geometry optimization by density functional theory calculations provided structures for the complexes that were used to calculate theoretical CCS with the ion trajectory method. A close match (337 Å2) was found for a single low Gibbs energy structure that displayed a binding pocket with Ser 2 and Ser 5 residues forming hydrogen bonds to the adrenaline catechol hydroxyls. Analysis of the BOMD trajectories revealed a small number of contacts between the incipient carbene carbon atom in the ligand and X-H bonds in the peptide, which was consistent with the lack of cross-linking. Temperature dependence of the internal dynamics of peptide S-adrenaline complexes as well as the specifics of the adrenaline carbene reactions are discussed. In particular, peptide amide hydrogen transfer to the carbene carbon atom was calculated to require crossing a potential energy barrier, which may hamper cross-linking in competition with carbene internal rearrangements.

Analysis of hyaluronan and its derivatives using chromatographic and mass spectrometric techniques.

The aim of this paper is to review chromatographic and mass-spectrometric methods and underline the best analytical approaches for successful analysis of various hyaluronic acid species in different types of samples. Hyaluronan-degrading enzymes and chemical depolymerization produce di- or oligosaccharides suitable for hyaluronan quantification or structural characterization of hyaluronan derivatives. Efficient purification and pre-column derivatization of hyaluronan disaccharides by reductive amination allow subnanogram quantification in biological samples. The chromatographic separation is capable to distinguish all glycosaminoglycans disaccharides and to resolve hyaluronan fragments with 2-40 monomers. Using electrospray ionization or matrix assisted laser desorption ionization, hyaluronan fragments up to 8 kDa or 41 kDa, respectively, can be observed. One- or two-dimensional chromatographic separation with higly sensitive mass-spectrometric detection is an indispensable tool for revealing substituent position, extent of modification and substitution patterns of chemically modified hyaluronan derivatives. It is essential for studying structure-biological function relationships of hyaluronan and its derivatives.

Signal enhancement in desorption nanoelectrospray ionization by custom-made inlet with pressure regulation.

The efficiency of desorption/ionization becomes more critical as the sampled surface area decreases. Desorption electrospray and desorption nanoelectrospray belong to ambient ionizations and enable direct surface analysis including mass spectrometric imaging. Lateral resolution in tens of micrometers was demonstrated for desorption nanoelectrospray previously, but sensitivity of the surface scan can be an issue. For desorption electrospray, the drag force in the source is driven by the flow of used gases and vacuum suction. Ion signal intensity can be improved by controlling the nebulizing gas flow rate or auxiliary pumping of a closed compartment in front of the mass spectrometer inlet. Because nanoelectrospray generates charged droplets without the assistance of a nebulizing gas, only vacuum suction drives the gas flow. In this study, the effect of pressure drop between the atmospheric and evacuated region of a mass spectrometer on the ion signal intensity was investigated for desorption nanoelectrospray. A modification of the commercial inlet was designed. An auxiliary pump was directly connected to an inner compartment of the modified mass spectrometer inlet through a needle valve that enabled the regulation of the reduced pressure. Adjustment of the pressure drop significantly increased signal intensity (more than one order of magnitude in some cases). To a lesser extent, the temperature of a heated capillary (an integral part of the inlet) also influenced the signal intensity. The applicability of desorption nanoelectrospray equipped with pressure regulation was demonstrated by the analysis of synthetic cathinones or a pill of paracetamol. Because pressure in the inlet depends on the diameters of orifices and the power of vacuum systems of mass spectrometers, the effect of the pressure regulation can be different for different instruments. Nevertheless, the presented results confirmed the importance of pressure drop-driven transport for desorption nanoelectrospray efficiency and can encourage its new applications.

Author Correction: Implementation of an efficient linear-optical quantum router.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Experimental kernel-based quantum machine learning in finite feature space.

We implement an all-optical setup demonstrating kernel-based quantum machine learning for two-dimensional classification problems. In this hybrid approach, kernel evaluations are outsourced to projective measurements on suitably designed quantum states encoding the training data, while the model training is processed on a classical computer. Our two-photon proposal encodes data points in a discrete, eight-dimensional feature Hilbert space. In order to maximize the application range of the deployable kernels, we optimize feature maps towards the resulting kernels' ability to separate points, i.e., their "resolution," under the constraint of finite, fixed Hilbert space dimension. Implementing these kernels, our setup delivers viable decision boundaries for standard nonlinear supervised classification tasks in feature space. We demonstrate such kernel-based quantum machine learning using specialized multiphoton quantum optical circuits. The deployed kernel exhibits exponentially better scaling in the required number of qubits than a direct generalization of kernels described in the literature.

Investigation of chromatographic peak broadening in supercritical fluid chromatography/atmospheric pressure chemical ionization mass spectrometry.

Multimode ionization source allows for switching between different ionization techniques, for example, electrospray and atmospheric pressure chemical ionization, within a single analysis. Supercritical fluid chromatography can handle a wide polarity range of substances from hydrophilic to lipophilic in a single run and can undoubtedly benefit from versatility of this ion source. Nevertheless, we observed a significant chromatographic peak broadening effect in atmospheric pressure chemical ionization mode during supercritical fluid chromatography-mass spectrometry analysis of volatile flavor compounds with a dual ion source named ESCi (Waters). Surprisingly, this effect was not related to the separation process but was triggered solely by the ion source conditions. Neither of photodiode array detector, electrospray mode nor a dedicated atmospheric pressure chemical ionization source suffered from such a phenomenon. Chromatographic peak profiles of ten test substances obtained with the dual ion source were compared with photodiode array detector data as a reference. The broadening effect was more pronounced for volatile compounds with low polarity. Dependence of peak broadening on the ion source settings was systematically investigated. Tuning of desolvation gas flow and its temperature dramatically reduced peak distortion and increased detection sensitivity.

Experimental hybrid quantum-classical reinforcement learning by boson sampling: how to train a quantum cloner.

We report on experimental implementation of a machine-learned quantum gate driven by a classical control. The gate learns optimal phase-covariant cloning in a reinforcement learning scenario having fidelity of the clones as reward. In our experiment, the gate learns to achieve nearly optimal cloning fidelity allowed for this particular class of states. This makes it a proof of present-day feasibility and practical applicability of the hybrid machine learning approach combining quantum information processing with classical control. The quantum information processing performed by the setup is equivalent to boson sampling, which, in complex systems, is predicted to manifest quantum supremacy over classical simulation of linear-optical setups.

Experimentally attacking quantum money schemes based on quantum retrieval games.

The concept of quantum money (QM) was proposed by Wiesner in the 1970s. Its main advantage is that every attempt to copy QM unavoidably leads to imperfect counterfeits. In the Wiesner's protocol, quantum banknotes need to be delivered to the issuing bank for verification. Thus, QM requires quantum communication which range is limited by noise and losses. Recently, Bozzio et al. (2018) have demonstrated experimentally how to replace challenging quantum verification with a classical channel and a quantum retrieval game (QRG). This brings QM significantly closer to practical realisation, but still thorough analysis of the revised scheme QM is required before it can be considered secure. We address this problem by presenting a proof-of-concept attack on QRG-based QM schemes, where we show that even imperfect quantum cloning can, under some circumstances, provide enough information to break a QRG-based QM scheme.