Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

Spectroscopy of hydrothermal reactions, 19: pH and salt dependence of decarboxylation of α‐alanine at 280–330°C in an FT‐IR spectroscopy flow reactor

The spontaneous decarboxylation of 0.5 m aqueous α‐alanine solutions as a function of pH (1–9 at 320°C, where neutrality is approximately 6) was determined with a flow reactor at 280–330°C and 275 bar by FT‐IR spectroscopy. The kinetics for the cationic and anionic forms have not been previously reported. The rate constants for the cationic form [CH₃(NH₃⁺)CHCO₂H], the anionic form [CH₃(NH₂)CHCO₂^?], and the zwitterion form [CH₃(NH₃⁺)CHCO₂^?] were obtained and followed the first‐order rate law. The rate of decarboxylation of the zwitterion is three times greater than that of the cationic and anionic forms in the temperature and pH ranges of study. The corresponding Arrhenius parameters were determined and compared with previously reported data. The addition of KCl (1 and 2 m) at the natural pH of α‐alanine resulted in a reduction of the decarboxylation rate, suggesting that the transition state is less polar than the zwitterion and/or that the activity of the zwitterion has been reduced. The α‐alanine solution is therefore somewhat more robust in solutions of high ionic strength, such as seawater, than it is in pure water. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 271–277, 2002     

Optimization of the abnormal Beckmann rearrangement: application to steroid 17-oximes

A novel and practical procedure was developed for the abnormal Beckmann rearrangement of steroid 17-oximes. Treatment of the 17-oximes with TFA/CH(OMe)(3) in boiling THF for 2 h gives the corresponding 13,17-seco alkene nitrile products in unprecedented high yields (70-92%). Since the alkene nitriles can be subsequently converted into 18-norsteroids, this general method provides a highly efficient route to these biologically important compounds and, by extension, to other structurally related natural products.     

Neutron activation analysis of gold and iridium in steel

A method of determination of trace gold and iridium in steel is presented. The samples were preconcentrated with an anion exchanger. The chemical recoveries were determined by an isotope tracer technique using¹⁹⁸Au and¹⁹²Ir.     

Energy transfer between photosynthetic units analyzed by flash oxygen yield vs. flash intensity

Abstract— Relative yield of O₂ (Y) was measured in Chlorella pyrenoidosa in response to varied intensity (l) of single 10μsec flashes on a constant low background of 710 nm light. Analysis is based on the proposition that the photochemical event leading to O₂ evolution occurs at a reaction center or trap which requires a time much longer than the flash for regeneration by dark reactions. Hence O₂, flash yield measures the number of traps ‘killed’ and allows treatment in terms of target theory. Data for Y vs. l were analyzed by computer fitting to four models. The first three models supposed that each unit (aggregate of light-harvesting pigment molecules) contains one, two, and three traps, respectively, and allows no transfer of excitation energy out of the unit. The last model supposed only one trap per unit and a probability of transfer out of a unit with closed trap. Among the first three models, the data best fit the one with two traps per unit. A slightly better fit for two traps per unit was obtained by introducing a trapping efficiency less than unity. An equally good fit was also obtained with the model of the Joliots with a probability of 0.3 that excitation energy in a unit with closed trap is transferred to another unit. Uncertainties in analysis arose from the necessity of treating maximum flash yield as an estimated parameter and by the possible inhomogeneity in units and traps.     

Unique spatial heterogeneity in ionic liquids

A multiscale coarse-graining model for ionic liquids has been extended to investigate the unique aggregation of cations in ionic liquids through computer simulation. It has been found that, with sufficiently long side chains, the tail groups of cations aggregate to form spatially heterogeneous domains, while headgroups of the cations and the anions distribute as uniformly as possible. This is understood as the result of competition between the charged electrostatic interactions between headgroups and anions and the collective short-range interactions between the neutral tail groups. This aggregation can help to explain a number of experimentally observed physical phenomena in ionic liquids.     

Optical properties of ZnO and ZnO:In nanorods assembled by sol-gel method

Self-assembled zinc oxide (ZnO) and indium-doping zinc oxide (ZnO:In) nanorod thin films were synthesized on quartz substrates without catalyst in aqueous solution by sol-gel method. The samples were characterized by x-ray diffraction (XRD), scanning electron microscope (SEM), Raman-scattering spectroscopy, room-temperature photoluminescence (PL) spectra, and temperature-dependent PL spectra measurements. XRD and Raman spectra illustrated that there were no single In2O3 phase in ZnO lattice after indium doping. The PL spectra of ZnO showed a strong UV emission band located at 394 nm and a very weak visible emission associated with deep-level defects. Indium incorporation induced the shift of optical band gap, quenching of the near-band-edge photoluminescence and enhanced LO mode multiphonon resonant Raman scattering in ZnO crystals at different temperatures. Abnormal temperature dependence of UV emission integrated intensity of ZnO and ZnO:In samples is observed. The local state emission peak of ZnO:In samples at 3.37 eV is observed in low-temperature PL spectra. The near-band-edge emission peak at room temperature was a mixture of excitons and impurity-related transitions for both of two samples.     

A novel support with artificially created recognition for the selective removal of proteins and for affinity chromatography

Summary Acrylamide and N,N-methylenebisacrylamide were copolymerized in the presence of a protein to form a gel which was pressed through a sieve. The gel particles obtained were packed into a chromatographic tube. The experimental conditions for the polymerization are such that the pores of the gel particles are large enough to permit the protein to diffuse out of the particles, so that the entrapped protein can be removed from the bed by washing with an aqueous solution. However the interaction with the matrix is so strong that the protein can be desorbed only by a buffer containing 0.5 M sodium chloride or by a 10% solution of acetic acid containing 10% SDS. When a sample containing the protein present during the polymerization was applied to the column along with other proteins this protein was the only one adsorbed. The technique worked selectively with hemoglobin, cytochrome C and transferrin.     

A thin-layer electrochemical detector coated with nafion film for liquid chromatography

The selectivity and analytical application of a thin-layer electrochemical detector comprised of glassy carbon electrode coated with Nafion film were investigated. As a result of the ion-exchange characteristics of the Nafion polymer, the selectivity and stability were improved greatly. The coated electrode has a good response only for cations with the same sensitivity as an uncoated (bare) electrode, but not for anions, and the response for neutral molecules is decreased three-fold. The diffusion of electroactive compounds in Nafion film is discussed based on the results of flow injection experiments. The peak current at the coated electrode was independent of the flow-rate of the mobile phase. Electrode poisoning due to protein adsorption was minimized. The use of 30% methanol or 10% acetonitrile in the mobile phase did not affect the performance of the coated electrode. Various analytes having three kinds of charge state, i.e., anionic, cationic and neutral, were tested. Liquid chromatography with electrochemical detection of ascorbic acid, norepinephrine, epinephrine, dopamine and uric acid was demonstrated.     

纳米分辨率的三维形貌检测仪

从光干涉方式，瞳窗关系和光源带宽等基本关系出发，利用空间不变系统理论解析了相移显微干涉检测系统中衍射效应的影响。为了减小横向分辨率对纵向分辨率的影响，利用相关信息提取或数字滤波的方法，获得了纳米分辨率的三维形貌。