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Laser desorption mass spectrometry and matrix-assisted laser desorption mass spectrometry (MALDI-MS) have been investigated for the analysis of a set of synthetic compounds containing one, two, five, eight or nine porphyrins. Intact singly ionized molecule ions were observed for each compound and the spectra were readily interpretable. The use of a matrix of 4-hydroxy-α-cyano-cinnamic acid greatly diminished the extent of fragmentation. Examination of the resulting mass spectra provides insight into aspects of the MALDI process. The present results show that high molecular weight photochemically active materials that absorb strongly at the wavelength of laser illumination can be analysed effectively and that MALDI-MS is a powerful analytical tool for synthetic chemistry of porphyrin-based molecules with dimensions ranging to 10 nm. The strong molecule ions observed for the largest compounds investigated (Zn₈-octamer, Zn₉-nonamer) indicates that this method should be applicable to even larger porphyrin arrays.

We investigated the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for analyzing porphyrinic compounds using a variety of different synthetic porphyrins, azaporphyrins, phthalocyanines and multiporphyrin arrays. Comparisons of spectra obtained from these analytes deposited either as neat samples or codeposited with neutral or acidic matrices have been made with the goal of identifying conditions that yield minimal demetalation, transmetalation, adduct formation and fragmentation. It was found that the molecular masses of many porphyrins can be successfully measured from neat sample preparations and do not require a matrix to facilitate desorption and ionization, although the measurement of large multiporphyrin arrays was facilitated by the use of matrices. Demetalation of magnesium porphyrins occurred in the presence of acidic matrices, but not with neutral matrices such as 1,4-benzoquinone. Positive ion spectra were obtained for each compound and negative ion spectra were also collected for the azaporphyrins and phthalocyanines. Examination of selected samples (prepared neat, with 1,4-benzoquinone, 2,3,5,6-tetrachloro-1,4-benzoquinone or α-cyano-4-hydroxycinnamic acid) showed that the dominant process of ionization involved oxidation yielding the radical cation M^+· rather than the protonated molecule [M+H]⁺. MALDI-TOF-MS is shown to be a powerful analytical tool for the characterization of diverse synthetic porphyrinic compounds.

Mass spectrometric studies of the composition of the gaseous phase under solid compounds of free phthalocyanine (H₂Pc) and its complexes with aluminium (AlClPc, AlFPc, (AlPc)₂O) and copper (CuPc) were performed in the temperature range up to 700 °C. It has been shown that the phthalocyanines sublime in the form of monomers, excluding one aluminium complex. All phthalocyanines under investigation sublime without thermal decomposition until 700 °C. The vapour pressure of these phthalocyanines was determined as a function of temperature by the Knudsen effusion method, in which the rate of effusion of the equilibrium vapour through a small orifice was measured. The thermodynamic parameters of the sublimation process for phthalocyanies were calculated.

A series of β-halogenated cationic metalloporphyrins were analyzed by LDI-TOF and ESI-MS. Although LDI-TOFMS reveals to be a good tool for the characterization of this family of metal-complexes, including the redox state of the metal, ESI-MS indicates in addition the relative tendency of such metal-complexes to be reduced.

In Biochemistry, tandem mass spectrometry (MS/MS) is the most common method for peptide and protein identifications. One computational method to get a peptide sequence from the MS/MS data is called de novo sequencing, which is becoming more and more important in this area. However De novo sequencing usually can only confidently determine partial sequences, while the undetermined parts are represented by "mass gaps". We call such a partially determined sequence a gapped sequence tag. When a gapped sequence tag is searched in a database for protein identification, the determined parts should match the database sequence exactly, while each mass gap should match a substring of amino acids whose masses add up to the value of the mass gap. In such a case, the standard string matching algorithm does not work any more. In this paper, we present a new efficient algorithm to find the matches of gapped sequence tags in a protein database.

Perfluorinated chemicals (PFCs) have been widely used in various household products. Because of inactive C–F bond within its structure, most PFCs cannot be biologically degraded and tend to accumulate in the ecosystems once discharged into the environment through sewage effluent etc., necessitating low-cost treatment technologies for PFCs. We have worked on the electrolysis method in which PFCs in water are decomposed at moderate cost, and found that perfluorooctane sulfonate, considered to be the most recalcitrant chemical among PFCs, can be decomposed by electrolysis. The decomposition products, however, remained unknown although we used various advanced analytical techniques (mass spectrometry for analysis of organic substances in liquid and gas samples, and combustion-ion chromatography for total fluorine analysis) to identify the products. The emanation of volatile low-molecular fluorine compounds was suspected. The present report summarizes our trial to identify the unknown decomposition products by analytical instruments cited above, and the application of PIXE/PIGE analysis to track the fluorine compounds lost from the solution by concentrating the gaseous compounds in low temperature (–100°C) activated charcoal.

The objective of the present study was to better understand the photophysics of explosives and chemical warfare simulants in order to develop better performing analytical tools. Photoionization mass spectra were taken using three optical schemes. The first was resonance-enhanced multiphoton ionization (REMPI) using few-ns duration 248 or 266 nm laser pulses. The second scheme was non-resonant multiphoton ionization (MPI) using 100 fs duration laser pulses at wavelengths between 325 and 795. The third approach was single photon ionization (SPI) using few-ns duration 118 nm laser pulses. For all the molecules investigated, mass spectra resulting exposure to ns-duration 248 or 266 nm laser pulses consisted of only low molecular weight fragments. Using fs-duration laser pulses produced more complicated, potentially analyzable, fragmentation patterns, usually with some parent peak. Single photon ionization gave the best results, with mass spectra consisting of almost only parent peak, except for the case of TATP.

Medicinal herbs have a long history of use in the practice of traditional Chinese medicine and a substantial body of evidence has, over recent decades, demonstrated a range of important pharmacological properties. Western biomedical researchers are examining not only the efficacy of the traditional herbal products but, through the use of a range of bioassays and analytical techniques, are developing improved methods to isolate and characterize active components. This review briefly describes the different extraction methodologies used in the preparation of herbal extracts and reviews the utility of chromatography-mass spectrometry for the analysis of their active components. In particular, applications of gas or liquid chromatography with mass spectrometry for the isolation and characterization of active components of ginseng are critically assessed. The analysis of toxic substances from herb extracts with mass spectrometric techniques is also discussed along with the potential for mass spectrometric methods to investigate the proteomics of herbal extracts.

Proteomics technology is based on the vast analytical power for protein/peptide identification and quantification offered by modern mass spectrometry coupled with hyphenated separation techniques such as two-dimensional gel electrophoresis (2DE) and micro- or nano-scale multidimensional liquid chromatography. The rapid growth of proteomics field provides an array of new tools for the integration of traditional Chinese medicine (TCM) with modern technology and systems biology, and is potentially advancing the progress of modernization and internationalization of TCM. Cho, in this issue of the American Journal of Chinese Medicine, highlights the recent application of 2DE-based and bottom-up proteomics in Chinese medicine research, including the exploration of pharmacological mechanisms of the actions of TCM, the facilitation of herb authentication and identification, and the profiling of protein expression following acupuncture treatment in animal models. Recent development in proteomics has provided further refinement on the analysis of proteins posttranslational modifications as well as quantitative comparison of different proteomes, and enabled the study of proteomes of specific diseases or biological processes under clinically relevant conditions. It is conceivable that the application of technologies developed in proteomics, genomics and metabonomics in the clinical practice and basic research of Chinese medicine will eventually lead to the reconciliation and integration of TCM and contemporary medicine. Chinese medicine is fundamentally a highly personalized medicine; perhaps it is time to embrace the arrival of TCM OMICS era in Chinese medicine research.

We performed mass spectrometric imaging (MSI) to localize ginsenosides (Rb₁, Rb₂ or Rc, and Rf) in cross-sections of the Panax ginseng root at a resolution of 100 μm using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Tandem mass spectrometry (MS/MS) of alkali metal-adducted ginsenoside ions revealed structural information of the corresponding saccharides and aglycone. MALDI-MSI confirmed that ginsenosides were located more in the cortex and the periderm than that in the medulla of a lateral root. In addition, it revealed that localization of ginsenosides in a root tip (diameter, 2.7 mm) is higher than that in the center of the root (diameter, 7.3 mm). A quantitative difference was detected between localizations of protopanaxadiol-type ginsenoside (Rb₁, Rb₂, or Rc) and protopanaxatriol-type ginsenoside (Rf) in the root. This imaging approach is a promising technique for rapid evaluation and identification of medicinal saponins in plant tissues.

BOREXINO has set new standards in the field of ultra-low background experiments. Such a success was only possible by a strict quality control program during the construction phase of the experiment. In this paper, we describe how construction materials and auxiliary systems of the BOREXINO detector were screened for their residual radioactivity with unprecedented high sensitivity. The highly sensitive assay techniques developed for this purpose were also used to validate the purity of water and nitrogen used in the experiment. Moreover, we report on the production of ²²²Rn-free nitrogen and synthetic air with very low ²²²Rn concentration as well as on the successful search for commercial nitrogen with a particularly low concentration of argon and krypton.

The paper deals with space-charge interactions in the ion population trapped in the Orbitrap${}^{\mathrm{\text{TM}}}$ mass analyzer where the ions perform multiple quasi-harmonic oscillations in the axial direction. The many-particle problem for interacting ions is mathematically complicated and its solution, even numerical, is obstructed by the required precision of one per million to be maintained on a large number $(10^5-10^6)$ of oscillation periods. We develop a perturbation method based on the Bogoliubov–Krylov–Mitropolsky theory and derive averaged Hamiltonian equations in perturbations, which describe the evolution of the ions’ oscillation amplitudes and phases in so-called “slow” time. This approach provides a semi-analytical comprehensive model of resonant and nonresonant space-charge effects and allows fast and accurate numerical computation. Practical mitigation strategies for most deteriorating space-charge effects like coalescence and frequency shifts are considered.

Imbalanced dataset affects the learning of classifiers. This imbalance problem is almost ubiquitous in biological datasets. Resampling is one of the common methods to deal with the imbalanced dataset problem. In this study, we explore the learning performance by varying the balancing ratios of training datasets, consisting of the observed peptides and absent peptides in the Mass Spectrometry experiment on the different machine learning algorithms. It has been observed that the ideal balancing ratio has yielded better performance than the imbalanced dataset, but it was not the best as compared to some intermediate ratio. By experimenting using Synthetic Minority Oversampling Technique (SMOTE) at different balancing ratios, we obtained the best results by achieving sensitivity of 92.1%, specificity value of 94.7%, overall accuracy of 93.4%, MCC of 0.869, and AUC of 0.982 with boosted random forest algorithm. This study also identifies the most discriminating features by applying the feature ranking algorithm. From the results of current experiments, it can be inferred that the performance of machine learning algorithms for the classification tasks can be enhanced by selecting optimally balanced training dataset, which can be obtained by suitably modifying the class distribution.

This review summarizes recent studies on the catalytic CO oxidation on Iridium(111) surfaces. This was investigated experimentally under ultrahigh vacuum (UHV) conditions using mass spectroscopy to detect gaseous products and photoelectron emission microscopy (PEEM) to visualize surface species. The underlying reaction–diffusion system based on the Langmuir–Hinshelwood mechanism was analyzed numerically.

The existence of bistability for this surface reaction was shown in experiment. For the first time the effect of noise on a bistable surface reaction was examined. In a surface science experiment the effects on product formation and the development of spatio-temporal patterns on the surface were explored.

Steady state CO₂ rates were measured under constant flux of the CO + O mixture as a function of sample temperature (360 K < T < 700 K) and gas composition, characterized by the molar fraction of CO in the feed gas (0 ≤ Y ≤ 1). The reaction reveals bistability in a limited region of Y and T. A rate hysteresis with two steady state rates was observed for cycling Y up and down, one of high reactivity (upper rate, oxygen covered surface) and one of low reactivity (lower rate, CO covered surface). The position of the hysteresis loop shifts to higher Y values and decreases in width with increasing temperature. For small CO content in the feed gas the CO₂ rate is proportional to Y^3/2. At 500 K extremely slow Y cycling measurements (about 100 hours per direction) were done and showed that bistability still exists and no slowly changing transients were observed. The requirements for the speed with which experiments can be executed without producing experimental artifacts were explored. Since over-sampling alters the measured hysteresis loop, a maximum rate for changing the gas composition in Y cycling experiments was determined.

The influence of noise on the reaction rates and the formation of spatio-temporal patterns on the surface was explored by superposing noise of Gaussian white type on Y and on T. Noisy Y (deviation Δ Y) represents multiplicative and additive noise, noisy T (deviation Δ T) multiplicative noise only. Noisy T enters the reaction via the rate-determining step, the observed CO₂ rates become noisy for low temperatures (around 420 K) when the surface is dominantly oxygen covered (CO + O reaction step is rate-limiting) and for higher temperatures (around 500 K) when the surface is dominantly CO covered (CO desorption step is rate-limiting).

The effect of noisy Y was examined for a sample temperature of 500 K and is dependent on the selected average gas composition. In the regions with one steady state CO₂ rate (outside the hysteresis) the recorded rates were noisy. The probability distribution of the rates is Gaussian shaped for the upper rate (below hysteresis) and asymmetric for the lower rate (above hysteresis). For large noise strength bursts, short-time excursions to and above the upper rate, were observed.

Inside the hysteresis small noise made the steady state rates noisy, but above a Y-dependent Δ Y transients from the locally stable to the globally stable rate branch were observed. These transients take up to several ten thousand seconds and become faster with increasing noise. For larger Y noise strength bursts and switching between both steady state rates were detected.

Photoelectron emission microscopy (PEEM) was done to visualize spatio-temporal adsorbate patterns on the surface as expected from the observations in the CO₂ rate measurements. CO- and oxygen-covered regions on the Ir(111) surface are visible in PEEM images as gray and black areas as a consequence of their work function contrast. Islands of the adsorbate, corresponding to the globally stable branch, are formed in a background of the other one. The long transient times are the result of the extremely slow domain wall motion of these islands (around 0.05 μm s^-1). In the hysteresis region CO oxidation on Iridium(111) surfaces is dominated by domain formation and wall motion for small to moderate noise strength. The island density increases with noise, but the wall velocity is independent of applied Δ Y. For larger noise amplitudes, fast switching between oxygen- and CO-dominated surfaces is observed as well as nucleation and growth of the minority phase in the majority phase.

In the numerically analyzed reaction–diffusion system all parameters were taken from the experiment. Modeling the reaction–diffusion system shows qualitative up to quantitative agreement with the experimental observations. The length scale for the modeling grid is determined from wall velocity seen in the experiments.

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In the aim to realize an efficient resonant biosensor, gallium arsenide (GaAs) presents many advantages. In addition to its properties of transduction, GaAs is a crystal for which microfabrication processes were developed, conferring the possibility to miniaturize the device and integrate electronic circuit. Moreover, the biofunctionalization could be realized on the crystalline surface without layer deposition, constituting a real advantage to perform reusable sensor. The functionalization of GaAs surface was engaged in order to immobilize a protein monolayer on this substrate. Functionalization was done using a mixed self assembled monolayer of thiolate molecules. Characterizations at micro and nanoscale were performed to control the surface state, the establishment of thiolates self-assembled monolayer, the surface atomic composition and the topography of the GaAs substrate at the different steps of the process. Protein immobilization on thiolates modified GaAs was revealed through a detailed AFM study and in situ MALDI-TOF MS and MS/MS modified surface interrogations.

This article reviews quantum computing and quantum algorithms. Some insights into its potential in speeding up computations are covered, with emphasis on the use of Grover's Search. In the last section, we discuss applications of quantum algorithm to bioinformatics. In particular, the extension of quantum counting algorithm to protein mass spectra counting is proposed.

Proteomics research programs typically comprise the identification of protein content of any given cell, their isoforms, splice variants, post-translational modifications, interacting partners and higher-order complexes under different conditions. These studies present significant analytical challenges owing to the high proteome complexity and the low abundance of the corresponding proteins, which often requires highly sensitive and resolving techniques. Mass spectrometry plays an important role in proteomics and has become an indispensable tool for molecular and cellular biology. However, the analysis of mass spectrometry data can be a daunting task in view of the complexity of the information to decipher, the accuracy and dynamic range of quantitative analysis, the availability of appropriate bioinformatics software and the overwhelming size of data files. The past ten years have witnessed significant technological advances in mass spectrometry-based proteomics and synergy with bioinformatics is vital to fulfill the expectations of biological discovery programs. We present here the technological capabilities of mass spectrometry and bioinformatics for mining the cellular proteome in the context of discovery programs aimed at trace-level protein identification and expression from microgram amounts of protein extracts from human tissues.