Liquid matrices for analyses by UV-MALDI mass spectrometry

Data are presented for a pH-adjustable liquid UV-matrix-assisted laser desorption ionization (MALDI) matrix for mass spectrometry analysis. The liquid matrix system possesses high analytical sensitivity within the same order of magnitude as that achievable by the commonly used solid UV-MALDI matrices such as 2,5-dihydroxybenzoic acid but with improved spot homogeneity and reproducibility. The pH of the matrix has been adjusted by the addition of up to 0.35% trifluoroacetic acid and up to 200 mM ammonium bicarbonate, achieving an on-target pH range of 3.5-8.6. Alteration of the pH does not seem to affect the overall sample signal intensity or signal-to-noise ratio achievable, nor does it affect the individual peptide ion signals from a mixture of peptides with varying isoelectric points (p1). In addition, the pH adjustment has allowed for the performance of a tryptic digest within the diluted pH-optimized liquid matrix.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Particulate matter mass concentration (PM10) under different ventilation methods in classrooms

Recently, studies have shown that the classroom environment is very important for students' health and performance. Thus, the evaluation of indoor air quality (IAQ) in a classroom is necessary to ensure students' well-being. In this paper the emphasis is on airborne concentration of particulate matter (PM) in adult education rooms. The mass concentration of PM10 particulates was measured in two classrooms under different ventilation methods in the University of Reading, UK, during the winter period of 2008. In another study the measurement of the concentration of particles was accompanied with measurements of CO2 concentration in these classrooms but this study is the subject of another publication. The ambient PM10, temperature, relative humidity, wind speed and direction, and rainfall events were monitored as well. In general, this study showed that outdoor particle concentrations and outdoor meteorological parameters were identified as significant factors influencing indoor particle concentration levels. Ventilation methods showed significant effects on air change rate and on indoor/outdoor (I/O) concentration ratios. Higher levels of indoor particulates were seen during occupancy periods. I/O ratios were significantly higher when classrooms were occupied than when they were unoccupied, indicating the effect of both people presence and outdoor particle concentration levels. The concentrations of PM10 indoors and outdoors did not meet the requirements of WHO standards for PM10 annual average.

The effects of mass loading the ossicles with a floating mass transducer on middle ear transfer function

Hypothesis: The aim of this study was to measure the mass loading effect of an active middle-ear implant (the Vibrant Soundbridge) in cadaver temporal bones. Background: Implantable middle ear hearing devices such as Vibrant Soundbridge have been used as an alternative to conventional hearing aids for the rehabilitation of sensorineural hearing loss. Other than the obvious disadvantage of requiring implantation middle ear surgery, it also applies a direct weight on the ossicular chain which, in turn, may have an impact on residual hearing. Previous studies have shown that applying a mass directly on the ossicular chain has a damping effect on its response to sound. However, little has been done to investigate the magnitude and the frequency characteristics of the mass loading effect in devices such as the Vibrant Soundbridge. Methods: Five fresh cadaver temporal bones were used. The stapes displacement was measured using laser Doppler vibrometry before and after the placement of a Vibrant Sound-bridge floating mass transducer. The effects of mass and attachment site were compared with the unloaded response. Measurements were obtained at frequencies between 0.1 and 10 kHz and at acoustic input levels of 100 dB sound pressure level. Each temporal bone acted as its own control. Results: Placement of the floating mass transducer caused a reduction of the stapes displacement. There were variations between the bones. The change of the stapes displacement varied from 0 dB to 28 dB. The effect was more prominent at frequencies above 1,000 Hz. Placing the floating mass transducer close to the incudostapedial joint reduced the mass loading effect. Conclusion: The floating mass transducer produces a measurable reduction of the stapes displacement in the temporal bone model. The effect is more prominent at high frequencies.

Development of a liquid chromatographic time-of-flight mass spectrometric method for the determination of unlabelled and deuterium-labelled alpha-tocopherol in blood components

A method is described for the analysis of deuterated and undeuterated alpha-tocopherol in blood components using liquid chromatography coupled to an orthogonal acceleration time-of-flight (TOF) mass spectrometer. Optimal ionisation conditions for undeuterated (d0) and tri- and hexadeuterated (d3 or d6) alpha-tocopherol standards were found with negative ion mode electrospray ionisation. Each species produced an isotopically resolved single ion of exact mass. Calibration curves of pure standards were linear in the range tested (0-1.5 muM, 0-15 pmol injected). For quantification of d0 and d6 in blood components following a standard solvent extraction, a stable-isotope-labelled internal standard (d3-alpha-tocopherol) was employed. To counter matrix ion suppression effects, standard response curves were generated following identical solvent extraction procedures to those of the samples. Within-day and between-day precision were determined for quantification of d0- and d6-labelled alpha-tocopherol in each blood component and both averaged 3-10%. Accuracy was assessed by comparison with a standard high-performance liquid chromatography (HPLC) method, achieving good correlation (r(2) = 0.94), and by spiking with known concentrations of alpha-tocopherol (98% accuracy). Limits of detection and quantification were determined to be 5 and 50 fmol injected, respectively. The assay was used to measure the appearance and disappearance of deuterium-labelled alpha-tocopherol in human blood components following deuterium-labelled (d6) RRR-alpha-tocopheryl acetate ingestion. The new LC/TOFMS method was found to be sensitive, required small sample volumes, was reproducible and robust, and was capable of high throughput when large numbers of samples were generated. Copyright (C) 2003 John Wiley Sons, Ltd.

Mass spectrometric analysis of glucose-modified ribonuclease

RNase A (1 mM) was incubated with glucose (0.4 M) at 37°C for up to 14 days in phosphate buffer (0.2 M, pH 7.4), digested with trypsin and analysed by LC-MS. The major sites of fructoselysine formation were Lys1, Lys7, Lys37 and Lys41. Three of these sites (Lys7, Lys37 and Lys41) were also the major sites of Ne-(carboxymethyl)lysine formation.

Vibrio parahaemolyticus associated with mass mortality of postlarval abalone, Haliotis diversicolor supertexta (L.), in Sanya, China

Outbreaks of mass mortality in postlarval abalone, Haliotis diversicolor supertexta (L.), have swept across south China since 2002 and in turn have resulted in many abalone farms closing. Twenty-five representative bacterial isolates were isolated from a sample of five diseased postlarval abalone, taken 15 d postfertilization during an outbreak of postlarval disease in Sanya, Hainan Province, China in October 2004. A dominant isolate, referred to as Strain 6, was found to be highly virulent to postlarvae in an experimental challenge test, with a 50% lethal dose (LD50) value of 3.2 x 10(4) colony forming units (CFU)/mL, while six of the other isolates were weakly virulent with LD50 values ranging from 1 x 10(6) to 1 x 10(7) CFU/mL, and the remaining 18 isolates were classified as avirulent with LD50 values greater than 1 x 10(8) CFU/mL. Using both an API 20E kit and 16S recombinant DNA sequence analysis, Strain 6 was shown to be Vibrio parahaemolyticus. It was sensitive to 4 and intermediately sensitive to 5 of the 16 antibiotics used when screening the antibiotic sensitivities of the bacterium. Extracellular products (ECPs) prepared from the bacterium were lethal to postlarvae when used in a toxicity test at a concentration of 3.77 mg protein/mL, and complete liquefaction of postlarvae tissues occurred within 24 h postexposure. Results from this study implicate V. parahaemolyticus as the pathogen involved in the disease outbreaks in postlarval abalone in Sanya and show that the ECPs may be involved in the pathogenesis of the disease.

Analysis of chain and blood group type and branching pattern of sialylated oligosaccharides by negative ion electrospray tandem mass spectrometry

We previously reported sequence determination of neutral oligosaccharides by negative ion electrospray tandem mass spectrometry on a quadrupole-orthogonal time-of-flight instrument with high sensitivity and without the need of derivatization. In the present report, we extend our strategies to sialylated oligosaccharides for analysis of chain and blood group types together with branching patterns. A main feature in the negative ion mass spectrometry approach is the unique double glycosidic cleavage induced by 3-glycosidic substitution, producing characteristic D-type fragments which can be used to distinguish the type 1 and type 2 chains, the blood group related Lewis determinants, 3,6-disubstituted core branching patterns, and to assign the structural details of each of the branches. Twenty mono- and disialylated linear and branched oligosaccharides were used for the investigation, and the sensitivity achieved is in the femtomole range. To demonstrate the efficacy of the strategy, we have determined a novel complex disialylated and monofucosylated tridecasaccharide that is based on the lacto-N-decaose core. The structure and sequence assignment was corroborated by :methylation analysis and H-1 NMR spectroscopy.

Geodetic mass balance of Azarova glacier, Kodar Mountains, eastern Siberia, and its links to observed and projected climatic change

The Kodar Mountains in eastern Siberia accommodate 30 small, cold-based glaciers with a combined surface area of about 19 km2. Very little is known about these glaciers, with the first survey conducted in the late 1950s. In this paper, we use terrestrial photogrammetry to calculate changes in surface area, elevation, volume and geodetic mass balance of the Azarova Glacier between 1979 and 2007 and relate these to meteorological data from nearby Chara weather station (1938-2007). The glacier surface area declined by 20±6.9% and surface lowered on average by 20±1.8 m (mean thinning: 0.71 m a-1) resulting in a strongly negative cumulative and average mass balance of -18±1.6 m w.e. and -640±60 mm w.e.a-1 respectively. The July-August air temperature increased at a rate of 0.036oC a-1 between 1979 and 2007 and the 1980-2007 period was, on average, around 1oC warmer than 1938-1979. The regional climate projections for A2 and B2 CO2 emission scenarios developed using PRECIS regional climate model indicate that summer temperatures will increase in 2071–2100 by 2.6-4.7°C and 4.9-6.2°C respectively in comparison with 1961–1990. The annual total of solid precipitation will increase by 20% under B2 scenario but decline by 3% under A2 scenario. The length of the ablation season will extend from July–August to June-September. The Azarova Glacier exhibits high sensitivity to climatic warming due to its low elevation, exposure to comparatively high summer temperatures, and the absence of a compensating impact of cold season precipitation. Further summer warming and decline of solid precipitation projected under the A2 scenario will force Azarova to retreat further while impacts of an increase in solid precipitation projected under the B2 scenario require further investigation.

Estimating relationships between air mass origin and chemical composition

Observations of a chemical at a point in the atmosphere typically show sudden transitions between episodes of high and low concentration. Often these are associated with a rapid change in the origin of air arriving at the site. Lagrangian chemical models riding along trajectories can reproduce such transitions, but small timing errors from trajectory phase errors dramatically reduce the correlation between modeled concentrations and observations. Here the origin averaging technique is introduced to obtain maps of average concentration as a function of air mass origin for the East Atlantic Summer Experiment 1996 (EASE96, a ground-based chemistry campaign). These maps are used to construct origin averaged time series which enable comparison between a chemistry model and observations with phase errors factored out. The amount of the observed signal explained by trajectory changes can be quantified, as can the systematic model errors as a function of air mass origin. The Cambridge Tropospheric Trajectory model of Chemistry and Transport (CiTTyCAT) can account for over 70% of the observed ozone signal variance during EASE96 when phase errors are side-stepped by origin averaging. The dramatic increase in correlation (from 23% without averaging) cannot be achieved by time averaging. The success of the model is attributed to the strong relationship between changes in ozone along trajectories and their origin and its ability to simulate those changes. The model performs less well for longer-lived chemical constituents because the initial conditions 5 days before arrival are insufficiently well known.

The effects of variation in snow properties on snow mass estimation using the Chang algorithm

Estimating snow mass at continental scales is difficult but important for understanding landatmosphere interactions, biogeochemical cycles and Northern latitudes’ hydrology. Remote sensing provides the only consistent global observations, but the uncertainty in measurements is poorly understood. Existing techniques for the remote sensing of snow mass are based on the Chang algorithm, which relates the absorption of Earth-emitted microwave radiation by a snow layer to the snow mass within the layer. The absorption also depends on other factors such as the snow grain size and density, which are assumed and fixed within the algorithm. We examine the assumptions, compare them to field measurements made at the NASA Cold Land Processes Experiment (CLPX) Colorado field site in 2002–3, and evaluate the consequences of deviation and variability for snow mass retrieval. The accuracy of the emission model used to devise the algorithm also has an impact on its accuracy, so we test this with the CLPX measurements of snow properties against SSM/I and AMSR-E satellite measurements.

Highly accurate detection of ovarian cancer using CA125 but limited improvement with serum matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling

Objectives: Our objective was to test the performance of CA125 in classifying serum samples from a cohort of malignant and benign ovarian cancers and age-matched healthy controls and to assess whether combining information from matrix-assisted laser desorption/ionization (MALDI) time-of-flight profiling could improve diagnostic performance. Materials and Methods: Serum samples from women with ovarian neoplasms and healthy volunteers were subjected to CA125 assay and MALDI time-of-flight mass spectrometry (MS) profiling. Models were built from training data sets using discriminatory MALDI MS peaks in combination with CA125 values and tested their ability to classify blinded test samples. These were compared with models using CA125 threshold levels from 193 patients with ovarian cancer, 290 with benign neoplasm, and 2236 postmenopausal healthy controls. Results: Using a CA125 cutoff of 30 U/mL, an overall sensitivity of 94.8% (96.6% specificity) was obtained when comparing malignancies versus healthy postmenopausal controls, whereas a cutoff of 65 U/mL provided a sensitivity of 83.9% (99.6% specificity). High classification accuracies were obtained for early-stage cancers (93.5% sensitivity). Reasons for high accuracies include recruitment bias, restriction to postmenopausal women, and inclusion of only primary invasive epithelial ovarian cancer cases. The combination of MS profiling information with CA125 did not significantly improve the specificity/accuracy compared with classifications on the basis of CA125 alone. Conclusions: We report unexpectedly good performance of serum CA125 using threshold classification in discriminating healthy controls and women with benign masses from those with invasive ovarian cancer. This highlights the dependence of diagnostic tests on the characteristics of the study population and the crucial need for authors to provide sufficient relevant details to allow comparison. Our study also shows that MS profiling information adds little to diagnostic accuracy. This finding is in contrast with other reports and shows the limitations of serum MS profiling for biomarker discovery and as a diagnostic tool

Evaluation of peak-picking algorithms for protein mass spectrometry

Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves.