Enhancement of mass spectrometry performance for proteomic analyses using highfield asymmetric waveform ion mobility spectrometry (FAIMS)

Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high‐field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co‐eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label‐free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments. Copyright © 2015 John Wiley & Sons, Ltd.     

Impedance based DNA chip for direct T(m) measurement

Si/SiO(2) chips were used to detect the hybridization of immobilized Oligo d(T)(20) through impedance measurement. The immobilization procedure involved an aminopropyl silane grafted silicon oxide surface activated by glutaraldehyde and subsequently modified by an aminolinker supporting oligonucleotides. The immobilization procedure was optimized and, in the best conditions, the hybridization of the immobilized oligonucleotide was able to generate a 50 Omega impedance change at an applied dc potential of -300 mV. The optimized DNA sensor was then used to directly determine the immobilized oligonucleotide T(m) via impedance measurement in a continuous temperature control flow system. A reproducible and specific 65 Omega impedance change was observed at 32 degrees C with a step duration as low as 15 min. This value compared well with the 31.4 degrees C theoretical value calculated from the sequence base pair composition and length.     

Ge(Li) gamma-ray spectrometry as a pilot for NaI(Tl) gamma-ray spectrometry

Lithium-drifted germanium semiconductor detectors give much better resolution than do thallium-activated sodium iodide detectors, but much lower sensitivity. They can often advantageously be used in conjunction with NaI(Tl) detectors, to show whether corrections must be applied for activities other than the one to be measured and to provide the necessary information for calculation of the corrections.     

Grazing-exit X-ray spectrometry for surface and thin-film analyses.

Electron-probe x-ray micro analysis (EPMA) and particle-induced x-ray emission analysis (PIXE) were performed under grazing-exit conditions. To control the exit angle (take-off angle), a new sample holder having a stepping motor was developed for grazing-exit EPMA. A carefully polished surface of a stainless-steal sample was measured. The surface of stainless steel is normally covered with a thin native oxide layer. The intensity ratio of Cr K(alpha) to Fe K(alpha) increases significantly at the grazing angle, becoming about 5-times larger at 0.2 degrees than at 40 degrees. This result indicates that grazing-exit EPMA is useful for surface analysis. In addition, a new PIXE equipment was developed for grazing-exit x-ray measurements. The sample is fixed and the x-ray detector is moved by applying a linear stage. Preliminary experimental results of grazing-exit PIXE are also shown.     

Expansion of repertoire of modified DNAs prepared by PCR using KOD Dash DNA polymerase

Thymidine analogues bearing a variety of functional groups at the C5-position via an amino-linker arm were prepared and the substrate activity for PCR using thermophilic KOD Dash DNA polymerase was examined. The enzyme accepted the thymidine analogues bearing pyridine, imidazole, biotin, a cationic-charged guanidinium, a cationic-charged amino, mercaptopyridyl and phenanthrolne groups at the C5-position, forming the corresponding PCR product. However, a thymidine analogue bearing a carboxyl group at the C5-position was a poor substrate and the corresponding PCR products could not be obtained. The thymidine analogue bearing a mercapto group was also a poor substrate for the enzyme, because it dimerized by disulfide linkage under PCR conditions. The enzyme hardly accepts the thymidine analogues with a negatively-charged carboxyl group or a bulky group as a substrate. KOD Dash DNA polymerase, having a broader substrate specificity than any other DNA polymerase, will expand the variety of modified DNAs that can be prepared by PCR.     

Advantages of high-resolution and high-mass range magnetic-sector mass spectrometry for electrospray ionization

Electrospray ionization (ESI) mass spectra have been measured on a magnetic-sector double-focusing mass spectrometer for a number of proteins and peptides. It is pointed out how in theory raising the mass resolution of a mass spectrometer from 800–1000 to 2400–3000 significantly increases the precision with which the envelope of isotopic peaks of a protein ion (or other organic ion) can be defined, particularly at higher masses. Better definition of the isotopic envelope ought to lead to higher precision in the experimental determination of molecular mass, which has been demonstrated. It is shown how ESI mass spectra of high-mass molecules are significantly less congested at higher m/z values, so that for these molecules (RMM > 40 000) there is an advantage in being able to record peaks at higher m/z values (m/z > 2000) representing ions with fewer charges. Fragmentation of a small peptide in the ESI source has been found to provide sequence information.     

基于DNA聚合酶I的新型电化学传感器及其胰腺癌K-ras基因点突变检测

本文构建DNA聚合酶I的新型DNA电化学传感器,将捕获探针通过Au-S键固定于Au基底表面,与互补靶序列杂交至点突变前一个碱基,通过DNA聚合酶Ⅰ将dUTP-biotin连接在目标DNA的检测位点,再与avidin-HRP反应,而后测定在TMB溶液中的电化学特性. 结果表明,DNA电化学传感电极的检测电流值与K-ras突变型基因浓度（1.0×10^-15 ~ 1.0×10^-10 mol·L^-1）对数呈良好的线性关系,且灵敏度高,特异性较佳.     

Drug Repurposing for Influenza Virus Polymerase Acidic (PA) Endonuclease Inhibitor

Drug repurposing can quickly and effectively identify novel drug repurposing opportunities. The PA endonuclease catalytic site has recently become regarded as an attractive target for the screening of anti-influenza drugs. PA N-terminal (PA_N) inhibitor can inhibit the entire PA endonuclease activity. In this study, we screened the effectivity of PA_N inhibitors from the FDA database through in silico methods and in vitro experiments. PA_N and mutant PA_N-I38T were chosen as virtual screening targets for overcoming drug resistance. Gel-based PA endonuclease analysis determined that the drug lifitegrast can effectively inhibit PA_N and PA_N-I38T, when the IC₅₀ is 32.82 ± 1.34 μM and 26.81 ± 1.2 μM, respectively. Molecular docking calculation showed that lifitegrast interacted with the residues around PA or PA-I38 T’s active site, occupying the catalytic site pocket. Both PA_N/PA_N-I38T and lifitegrast can acquire good equilibrium in 100 ns molecular dynamic simulation. Because of these properties, lifitegrast, which can effectively inhibit PA endonuclease activity, was screened through in silico and in vitro research. This new research will be of significance in developing more effective and selective drugs for anti-influenza therapy.     

Biochemical Properties and PCR Performance of a Family B DNA Polymerase from Hyperthermophilic Euryarchaeon <Emphasis Type="Italic">Thermococcus peptonophilus</Emphasis>

The Thermococcus peptonophilus (Tpe) DNA polymerase gene was expressed under the control of the T7lac promoter on pET-22b(+) in Escherichia coli BL21-CodonPlus(DE3)-RIL in order to fully elucidate its biochemical properties and evaluate its feasibility in polymerase chain reaction (PCR) application. The expressed enzyme was then purified by heat treatment followed by two steps of column chromatography after which optimum pH and temperature of the enzyme were evaluated to be 7.0 and 75 °C, respectively. The optimal buffer for PCR with Tpe DNA polymerase consisted of 50 mM Tris–HCl (pH 8.0), 2 mM MgCl₂, 80 mM KCl, and 0.02% Triton X-100. Tpe DNA polymerase revealed a 3.6-fold higher fidelity (3.37 × 10⁻⁶) than Taq DNA polymerase (12.13 × 10⁻⁶) and performed significantly more efficiently in PCR amplification than both Taq and Pfu DNA polymerases. Ratios of 31:1 of Taq to Tpe DNA polymerases allowed PCR amplification of targets up to 15 kb in length with a 2.2-fold higher fidelity than Taq DNA polymerase. The results of the PCR experiments indicate that Tpe DNA polymerase may provide a higher fidelity DNA amplification in a shorter reaction time.     

Interactive programme for evaluation of circular analyses (IPECA)

A PC-based interactive programme is described which is designed to help in suggesting the best estimate of the true value of an analyte content from results of collective studies aiming at deriving consensus values and/or reference material preparation by employing combined statistical and analytical considerations. The Grubbs, Dixon, Huber tests, and the coefficients of skewness and curtosis tests are used for outlier detection, the Bartlett, Cochran, and the standard error tests are employed for testing variance homogeneity testing and/or variance outliers identification, while the normality of results distribution is tested according to the Kolmogoroff-Smirnoff-Lilliefors and Shapiro-Wilk tests. One-way analysis of variance (ANOVA) is employed to test differences among means of results obtained in different conditions (laboratories, analytical methods, etc.) and to calculate the overall mean and its confidence interval accordingly. Points for an analytical discussion are given which should be considered prior to a decision whether a result of a trace element determination, identified as an outlier from statistical reasons, should be rejected.     

Laserspray ionization (LSI) ion mobility spectrometry (IMS) mass spectrometry

A simple device is described for desolvation of highly charged matrix/analyte clusters produced by laser ablation leading to multiply charged ions that are analyzed by ion mobility spectrometry-mass spectrometry. Thus, for example, highly charged ions of ubiquitin and lysozyme are cleanly separated in the gas phase according to size and mass (shape and molecular weight) as well as charge using Tri-Wave ion mobility technology coupled to mass spectrometry. This contribution confirms the mechanistic argument that desolvation is necessary to produce multiply charged matrix-assisted laser desorption/ionization (MALDI) ions and points to how these ions can be routinely formed on any atmospheric pressure mass spectrometer.     

DNA assay based on monolayer-barcoded nanoparticles for mass spectrometry in combination with magnetic microprobes

Mass spectrometry (MS) based methodology offers simple, fast and sensitive diagnosis. While it has become the predominate approach in biomolecular analysis, it has not been suitable for analyzing nucleic acid due to its low ionization efficiency. We report herein on a DNA assay based on monolayer-barcoded nanoparticles that were encoded with reporter mass molecules, which act as surrogate molecules for the matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF MS) identification of target DNA through mass spectrometry in combination with magnetic microprobes. This assay demonstrated high MS sensitivity, with the ability to detect target DNA at femtomolar (10⁻¹⁵ M) levels. This inaugural effort using combined techniques is significant because it showed an extraordinary analytical capability for differentiating the single nucleotide polymorphism (SNP), which comprises the most abundant source of genetic variation in the human genome. We also report herein the feasibility of MS detection of two target DNAs that have the same mass but different nucleotide base composition, which classic MS methodology is inherently unable to differentiate.     

Nano-structured nickel oxide based DNA biosensor for detection of visceral leishmaniasis (Kala-azar)

Sol-gel synthesized nickel oxide (NiO) film deposited onto indium tin oxide (ITO) coated glass plate has been utilized for the development of sensitive and stable DNA biosensor and demonstrated for diagnosis of visceral leishmaniasis also known as Kala-azar. Leishmania specific sensor is developed by immobilizing 23mer DNA sequence (oligonucleotide) identified from 18S rRNA gene sequences from Leishmania donovani. Characterization studies like X-Ray Diffraction and Scanning Electron Microscopy revealed the formation of nano-structured NiO, while immobilization of single strand (ss)-DNA of Leishmania was supported by UV-visible, Fourier Transform Infrared Spectroscopy and Scanning Electron Microscopy techniques. Response studies of ss-DNA/NiO/ITO bioelectrode are carried out using differential pulsed voltammetry in presence of methylene blue redox dye as a redox mediator. A linear response is obtained in the wide concentration range of 2 pg ml(-1) to 2 μg ml(-1) of complementary target genomic DNA (disease DNA) within the variation of 10% for 5 sets of studies. The observed results hold promise not only for diagnosis of Kala-azar patients but also hold enormous potential of the nano-NiO based probe for development of stable and sensitive biosensors.     

Advantages and limitations of thermal lens spectrometry over conventional spectrophotometry for absorbance measurements

This review considers the advantages and the limitations that thermal lens spectrometry has over conventional spectrophotometry for the measurement of optical absorption in specific applications. The photothermal method is characterized by its intrinsic sensitivity resulting from the indirect nature of the measurement and amplified by physical and thermo-optical parameters which are not effective in absorbance measurements. Other advantages include a weak dependence on light scattering and the complementary nature of photothermal spectra with respect to absorption and emission spectra for speciation studies at very low concentrations. The main drawbacks are the convective noise, the background absorbance and the complexity of the experimental set-up, especially when differential or wavelength scanning measurements are required.     

Advantages and drawbacks of nanospray for studying noncovalent protein-DNA complexes by mass spectrometry

The noncovalent complexes between the BlaI protein dimer (wild-type and GM2 mutant) and its double-stranded DNA operator were studied by nanospray mass spectrometry and tandem mass spectrometry (MS/MS). Reproducibility problems in the nanospray single-stage mass spectra are emphasized. The relative intensities depend greatly on the shape of the capillary tip and on the capillary-cone distance. This results in difficulties in assessing the relative stabilities of the complexes simply from MS(1) spectra of protein-DNA mixtures. Competition experiments using MS/MS are a better approach to determine relative binding affinities. A competition between histidine-tagged BlaIWT (BlaIWTHis) and the GM2 mutant revealed that the two proteins have similar affinities for the DNA operator, and that they co-dimerize to form heterocomplexes. The low sample consumption of nanospray allows MS/MS spectra to be recorded at different collision energies for different charge states with 1 microL of sample. The MS/MS experiments on the dimers reveal that the GM2 dimer is more kinetically stable in the gas phase than the wild-type dimer. The MS/MS experiments on the complexes shows that the two proteins require the same collision energy to dissociate from the complex. This indicates that the rate-limiting step in the monomer loss from the protein-DNA complex arises from the breaking of the protein-DNA interface rather than the protein-protein interface. The dissociation of the protein-DNA complex proceeds by the loss of a highly charged monomer (carrying about two-thirds of the total charge and one-third of the total mass). MS/MS experiments on a heterocomplex also show that the two proteins BlaIWTHis and BlaIGM2 have slightly different charge distributions in the fragments. This emphasizes the need for better understanding the dissociation mechanisms of biomolecular complexes.     

A rapid automated method for wine analysis based upon sequential injection (SI)-FTIR spectrometry

A new process control methodology for the simultaneous determination of sugars, alcohols and organic acids in wine based on multivariate evaluation of mid-IR transmission spectra of wine samples is presented. In addition to ethanol several lower level wine components (glucose, fructose, glycerol, citric-, tartaric-, malic-, lactic- and acetic acid) were determined. To establish a multivariate calibration model a set of 72 calibration solutions was prepared and measured, using a novel, fully automated sequential injection (SI) system with Fourier transform infrared (FTIR) detection. The resulting spectra were evaluated using a partial least square (PLS) model. The developed PLS model was then applied to the analysis of real wine samples containing 79–91 g L^–1 ethanol, 5.9–8.1 g L^–1 glycerol, 0.4–6.9 g L^–1 glucose, 1.5–7.5 g L^–1 fructose, 0.3–1.6 g L^–1 citric acid, 1.0–1.7 g L^–1 tartaric acid, 0.02–3.2 g L^–1 malic acid, 0.4–2.8 g L^–1 lactic acid and 0.15–0.60 g L^–1 acetic acid, yielding results which were in good agreement with those obtained by an external reference method (HPLC-IR). The short analysis time (less than 3 min) together with high reproducibility makes the newly developed method applicable to process control and screening purposes (average of the standard deviations calculated from four repetitive measurements of six different real samples: ethanol: 0.55 g L^–1, glycerol: 0.037 g L^–1, glucose: 0.056 g L^–1, fructose: 0.036 g L^–1, citric acid: 0.020 g L^–1, tartaric acid: 0.010 g L^–1, malic acid: 0.052 g L^–1, lactic acid: 0.012 g L^–1 and acetic acid: 0.026 g L^–1). Received: 21 January 1998 / Revised: 5 March 1998 / Accepted: 6 March 1998     

A rapid automated method for wine analysis based upon sequential injection (SI)-FTIR spectrometry

A new process control methodology for the simultaneous determination of sugars, alcohols and organic acids in wine based on multivariate evaluation of mid-IR transmission spectra of wine samples is presented. In addition to ethanol several lower level wine components (glucose, fructose, glycerol, citric-, tartaric-, malic-, lactic- and acetic acid) were determined. To establish a multivariate calibration model a set of 72 calibration solutions was prepared and measured, using a novel, fully automated sequential injection (SI) system with Fourier transform infrared (FTIR) detection. The resulting spectra were evaluated using a partial least square (PLS) model. The developed PLS model was then applied to the analysis of real wine samples containing 79–91 g L^–1 ethanol, 5.9–8.1 g L^–1 glycerol, 0.4–6.9 g L^–1 glucose, 1.5–7.5 g L^–1 fructose, 0.3–1.6 g L^–1 citric acid, 1.0–1.7 g L^–1 tartaric acid, 0.02–3.2 g L^–1 malic acid, 0.4–2.8 g L^–1 lactic acid and 0.15–0.60 g L^–1 acetic acid, yielding results which were in good agreement with those obtained by an external reference method (HPLC-IR). The short analysis time (less than 3 min) together with high reproducibility makes the newly developed method applicable to process control and screening purposes (average of the standard deviations calculated from four repetitive measurements of six different real samples: ethanol: 0.55 g L^–1, glycerol: 0.037 g L^–1, glucose: 0.056 g L^–1, fructose: 0.036 g L^–1, citric acid: 0.020 g L^–1, tartaric acid: 0.010 g L^–1, malic acid: 0.052 g L^–1, lactic acid: 0.012 g L^–1 and acetic acid: 0.026 g L^–1).