SciCombinator

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Concept: Ion source

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SELDI-TOF mass spectrometer’s compact size and automated, high throughput design have been attractive to clinical researchers, and the platform has seen steady-use in biomarker studies. Despite new algorithms and preprocessing pipelines that have been developed to address reproducibility issues, visual inspection of the results of SELDI spectra preprocessing by the best algorithms still shows miscalled peaks and systematic sources of error. This suggests that there continues to be problems with SELDI preprocessing. In this work, we study the preprocessing of SELDI in detail and introduce improvements. While many algorithms, including the vendor supplied software, can identify peak clusters of specific mass (or m/z) in groups of spectra with high specificity and low false discover rate (FDR), the algorithms tend to underperform estimating the exact prevalence and intensity of peaks in those clusters. Thus group differences that at first appear very strong are shown, after careful and laborious hand inspection of the spectra, to be less than significant. Here we introduce a wavelet/neural network based algorithm which mimics what a team of expert, human users would call for peaks in each of several hundred spectra in a typical SELDI clinical study. The wavelet denoising part of the algorithm optimally smoothes the signal in each spectrum according to an improved suite of signal processing algorithms previously reported (the LibSELDI toolbox under development). The neural network part of the algorithm combines those results with the raw signal and a training dataset of expertly called peaks, to call peaks in a test set of spectra with approximately 95% accuracy. The new method was applied to data collected from a study of cervical mucus for the early detection of cervical cancer in HPV infected women. The method shows promise in addressing the ongoing SELDI reproducibility issues.

Concepts: Human papillomavirus, Cervical cancer, Mass spectrometry, Clinical research, Ion source, Mass-to-charge ratio, Mass spectrometry software, Soft laser desorption

64

BACKGROUND: Psychological effects of air ions have been reported for more than 80 years in the media and scientific literature. This study summarizes a qualitative literature review and quantitative meta-analysis, where applicable, that examines the potential effects of exposure to negative and positive air ions on psychological measures of mood and emotional state. METHODS: A structured literature review was conducted to identify human experimental studies published through August, 2012. Thirty-three studies (1957–2012) evaluating the effects of air ionization on depression, anxiety, mood states, and subjective feelings of mental well-being in humans were included. Five studies on negative ionization and depression (measured using a structured interview guide) were evaluated by level of exposure intensity (high vs. low) using meta-analysis. RESULTS: Consistent ionization effects were not observed for anxiety, mood, relaxation/sleep, and personal comfort. In contrast, meta-analysis results showed that negative ionization, overall, was significantly associated with lower depression ratings, with a stronger association observed at high levels of negative ion exposure (mean summary effect and 95% confidence interval (CI) following high- and low-density exposure: 14.28 (95% CI: 12.93-15.62) and 7.23 (95% CI: 2.62-11.83), respectively). The response to high-density ionization was observed in patients with seasonal or chronic depression, but an effect of low-density ionization was observed only in patients with seasonal depression. However, no relationship between the duration or frequency of ionization treatment on depression ratings was evident. CONCLUSIONS: No consistent influence of positive or negative air ionization on anxiety, mood, relaxation, sleep, and personal comfort measures was observed. Negative air ionization was associated with lower depression scores particularly at the highest exposure level. Future research is needed to evaluate the biological plausibility of this association.

Concepts: Psychology, Ion, Ion source, Seasonal affective disorder, Emotion, Mood disorder, Ions, Air ioniser

28

Gamma-hydroxybutyric acid (GHB) and its “pro-drugs”, gamma-butyrolactone (GBL) and 1,4 butanediol (1,4-BD), are drugs of abuse with depressant effects on the central nervous system. Many analytical methods have been proposed for the quantitative determination of these compounds mainly in biological matrices but only few have been addressed to dietary supplements and foods. Facile synthesis of the GBL and 1,4-BD isotopologues are available by “one pot” Ru-catalyzed homogeneous deuteration of dicarboxylic acids. In this work we propose a new method for determination of GHB, GBL and 1,4-BD in commercially available dietary supplements, based on isotope dilution mass spectrometry (ID-MS). The procedure involves a simple extraction of sample with acidic acetonitrile and direct analysis by GC-ID-MS method without any purification or derivatization. Indeed, the proposed method takes advantage of the complete conversion of GHB (free acid or its salts) to GBL, allowing the quantification of GHB and its pro-drugs. Five levels for each calibration curve have been prepared by diluting working solutions of the analytes to obtain concentrations ranging from 1 to 20mg/mL. The validation procedures have shown an accuracy between 88% and 99% and a precision between 7.3% and 2.9% of each analyte in the sample matrix. Positive ions chemical ionization (PICI) have been employed to preserve the information on molecular ions and to improve specificity and sensitivity of quantitative determination.

Concepts: Nervous system, Acid, Ammonia, Mass spectrometry, Molecule, Chemistry, Analytical chemistry, Ion source

28

Direct analysis in real time (DART) is a novel ionization technique that has been demonstrated in numerous applications as a useful tool for fast and convenient mass spectrometry (MS)-based analysis of complex samples. In this study, the feasibility of DART ionization coupled to a high-resolution mass spectrometer utilizing an orbitrap mass analyzer (orbitrap MS) for high-throughput analysis of antiparasitic veterinary drugs was explored.

Concepts: Mass spectrometry, Ion source, Measuring instruments, Fast atom bombardment, Fourier transform ion cyclotron resonance, Ionization, DART ion source

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A new ionization technique: A radio-frequency signal was used to ionize neutral organic molecules in the ultrahigh-vacuum region of a Fourier transform ion cyclotron resonance mass spectrometer. Radio-frequency ionization (RFI) yielded S/N ratios roughly six times higher than those generated by the conventional 70 eV electron impact ionization (EI).

Concepts: Mass spectrometry, Ion, Scientific techniques, Fourier transform, Ion source, Fourier transform ion cyclotron resonance, Ion cyclotron resonance, Electron ionization

28

Fast MS techniques have been applied to the analysis of sulfur volatiles in Allium species and varieties to distinguish phenotypes. Headspace sampling by proton transfer reaction (PTR) MS and surface sampling by desorption electrospray ionization (DESI) MS were used to distinguish lachrymatory factor synthase (LFS)-silenced (tearless; LFS-) onions from normal, LFS active (tear-inducing; LFS+), onions. PTR-MS showed lower concentrations of the lachrymatory factor (LF, 3) and dipropyl disulfide 12 from tearless onions. DESI-MS of the tearless onions confirmed the decreased LF 3, and revealed much higher concentrations of the sulfenic acid condensates. Using DESI-MS with MS2 could distinguish zwiebelane ions from thiosulfinate ions. DESI-MS gave reliable fast phenotyping of LFS+ versus LFS- onions by simply scratching leaves and recording the extractable ions for <0.5 min. DESI-MS leaf compound profiles also allowed the rapid distinction of a variety of Allium cultivars to aid plant breeding selections.

Concepts: Mass spectrometry, Electrospray ionization, Taylor cone, Ion source, Electrospray, Protein mass spectrometry, Desorption electrospray ionization, Cultivar

28

Probe electrospray ionization (PESI) is a recently developed method that uses a sharp solid needle as electrospray emitter and the sample is loaded to the needle tip by repetitive movement of the needle probe. This method has been previously used for the analysis of sample with high salt concentration and real-world samples without sample pretreatment. Although PESI is also applicable to aqueous solution, the ion signal stability and reproducibility were not satisfactory due to the spontaneous occurrence of corona discharge taking place on the metallic needle tip.

Concepts: Concentration, Chemical properties, Chemistry, Solid, 1980s music groups, Ion source, Solutions, Aqueous solution

28

Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a relatively new imaging modality that allows mapping of a wide range of biomolecules within a thin tissue section. The technology uses a laser beam to directly desorb and ionize molecules from discrete locations on the tissue that are subsequently recorded in a mass spectrometer. IMS is distinguished by the capability to directly measure molecules in situ ranging from small metabolites to proteins, reporting hundreds to thousands of expression patterns from a single imaging experiment. This article reviews recent advances in IMS technology, applications, and experimental strategies that allow it to significantly aid in the discovery and understanding of molecular processes in biological and clinical samples.

Concepts: Molecular biology, Mass spectrometry, Chemistry, Proteomics, Ion source, Matrix-assisted laser desorption/ionization, MALDI imaging, Mass spectrometry imaging

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There are no effective clinical biomarkers for early and specific detection of lung cancer (LC). The changes in the levels of some serum metabolites of LC patients are associated with patient gender and LC stages.

Concepts: Cancer, Mass spectrometry, Lung cancer, Cancer staging, Fourier transform, Ion source, Fourier transform ion cyclotron resonance, Ion cyclotron resonance

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Conventional electrospray ionization mass spectrometry (ESI-MS) uses a capillary for sample loading and ionization. Along with the development of ambient ionization techniques, ESI-MS using noncapillary emitters has attracted more interest in recent years. Following our recent report on ESI-MS using wooden tips (Anal. Chem. 83, 8201-8207 (2011)), the technique was further investigated and extended in this study. Our results revealed that the wooden tips could serve as a chromatographic column for separation of sample components. Sequential and exhaustive ionization was observed for proteins and salts on wooden tips with salts ionized sooner and proteins later. Nonconductive materials that contain microchannels/pores could be used as tips for ESI-MS analysis with sample solutions loaded to the sharp-ends only, since rapid diffusion of sample solutions by capillary action would enable the tips to become conductive. Tips of inert materials such as bamboo, fabrics, and sponge could be used for sample loading and ionization, while samples such as tissue, mushroom, and bone could form tips to induce ionization for direct analysis with application of a high voltage. Figure.

Concepts: Mass spectrometry, Electrospray ionization, Taylor cone, Ion source, Electrospray, Protein mass spectrometry, John Bennett Fenn, Desorption electrospray ionization