Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

Probing the Allende meteorite with a miniature laser-ablation mass analyser for space application

We measured the elemental composition on a sample of Allende meteorite with a miniature laser ablation mass spectrometer. This Laser Mass Spectrometer (LMS) has been designed and built at the University of Bern in the Department of Space Research and Planetary Sciences with the objective of using such an instrument on a space mission. Utilising the meteorite Allende as the test sample in this study, it is demonstrated that the instrument allows the in situ determination of the elemental composition and thus mineralogy and petrology of untreated rocky samples, particularly on planetary surfaces. In total, 138 measurements of elemental compositions have been carried out on an Allende sample. The mass spectrometric data are evaluated and correlated with an optical image. It is demonstrated that by illustrating the measured elements in the form of mineralogical maps, LMS can serve as an element imaging instrument with a very high spatial resolution of µm scale. The detailed analysis also includes a mineralogical evaluation and an investigation of the volatile element content of Allende. All findings are in good agreement with published data and underline the high sensitivity, accuracy and capability of LMS as a mass analyser for space exploration.

Coupling of LMS with a fs-laser ablation ion source: elemental and isotope composition measurements

Mass spectrometric analysis of elemental and isotopic compositions of several NIST standards is performed by a miniature laser ablation/ionisation reflectron-type time-of-flight mass spectrometer (LMS) using a fs-laser ablation ion source (775 nm, 190 fs, 1 kHz). The results of the mass spectrometric studies indicate that in a defined range of laser irradiance (fluence) and for a certain number of accumulations of single laser shot spectra, the measurements of isotope abundances can be conducted with a measurement accuracy at the per mill level and at the per cent level for isotope concentrations higher and lower than 100 ppm, respectively. Also the elemental analysis can be performed with a good accuracy. The LMS instrument combined with a fs-laser ablation ion source exhibits similar detection efficiency for both metallic and non-metallic elements. Relative sensitivity coefficients were determined and found to be close to one, which is of considerable importance for the development of standard-less instruments. Negligible thermal effects, sample damage and excellent characteristics of the fs-laser beam are thought to be the main reason for substantial improvement of the instrumental performance compared to other laser ablation mass spectrometers.

Elemental and Lead Isotopic Data of Copper Finds from the Singen Cemetery, Germany – a Methodological Approach to Investigate Early Bronze Age Trade Networks

We report a trace element - Pb isotope analytical (LIA) database on the "Singen Copper", a peculiar type of copper found in the North Alpine realm, from its type locality, the Early Bronze Age Singen Cemetery (Germany). What distinguishes “Singen Copper” from other coeval copper types? (i) is it a discrete metal lot with a uniform provenance (if so, can its provenance be constrained)? (ii) was it manufactured by a special, unique metallurgical process that can be discriminated from others? Trace element concentrations can give clues on the ore types that were mined, but they can be modified (more or less intentionally) by metallurgical operations. A more robust indicator are the ratios of chemically similar elements (e.g. Co/Ni, Bi/Sb, etc.), since they should remain nearly constant during metallurgical operations, and are expected to behave homogeneously in each mineral of a given mining area, but their partition amongst the different mineral species is known to cause strong inter-element fractionations. We tested the trace element ratio pattern predicted by geochemical arguments on the Brixlegg mining area. Brixlegg itself is not compatible with the Singen Copper objects, and we only report it because it is a rare instance of a mining area for which sufficient trace element analyses are available in the literature. We observe that As/Sb in fahlerz varies by a factor 1.8 above/below median; As/Sb in enargite varies by a factor of 2.5 with a 10 times higher median. Most of the 102 analyzed metal objects from Singen are Sb-Ni-rich, corresponding to “antimony-nickel copper” of the literature. Other trace element concentrations vary by > 100 times, ratios by factors > 50. Pb isotopic compositions are all significantly different from each other. They do not form a single linear array and require > 3 ore batches that certainly do not derive from one single mining area. Our data suggest a heterogeneous provenance of “Singen copper”. Archaeological information limits the scope to Central European sources. LIA requires a diverse supply network from many mining localities, including possibly Brittany. Trace element ratios show more heterogeneity than LIA; this can be explained either by deliberate selection of one particular ore mineral (from very many sources) or by processing of assorted ore minerals from a smaller number of sources, with the unintentional effect that the quality of the copper would not be constant, as the metallurgical properties of alloys would vary with trace element concentrations.

Intracellular imaging of nanoparticles: is it an elemental mistake to believe what you see?

In order to understand how nanoparticles (NPs <100 nm) interact with cellular systems, potentially causing adverse effects, it is important to be able to detect and localize them within cells. Due to the small size of NPs, transmission electron microscopy (TEM) is an appropriate technique to use for visualizing NPs inside cells, since light microscopy fails to resolve them at a single particle level. However, the presence of other cellular and non-cellular nano-sized structures in TEM cell samples, which may resemble NPs in size, morphology and electron density, can obstruct the precise intracellular identification of NPs. Therefore, elemental analysis is recommended to confirm the presence of NPs inside the cell. The present study highlights the necessity to perform elemental analysis, specifically energy filtering TEM, to confirm intracellular NP localization using the example of quantum dots (QDs). Recently, QDs have gained increased attention due to their fluorescent characteristics, and possible applications for biomedical imaging have been suggested. Nevertheless, potential adverse effects cannot be excluded and some studies point to a correlation between intracellular particle localization and toxic effects. J774.A1 murine macrophage-like cells were exposed to NH2 polyethylene (PEG) QDs and elemental co-localization analysis of two elements present in the QDs (sulfur and cadmium) was performed on putative intracellular QDs with electron spectroscopic imaging (ESI). Both elements were shown on a single particle level and QDs were confirmed to be located inside intracellular vesicles. Nevertheless, ESI analysis showed that not all nano-sized structures, initially identified as QDs, were confirmed. This observation emphasizes the necessity to perform elemental analysis when investigating intracellular NP localization using TEM.

Eliminating exposure to aqueous solvents is necessary for the early detection and ultrastructural elemental analysis of sites of calcium and phosphorus enrichment in mineralizing UMR106-01 osteoblastic cultures

The mechanism underlying the mineralization of bone is well studied and yet it remains controversial. Inherent difficulties of imaging mineralized tissues and the aqueous solubility of calcium and phosphate, the 2 ions which combine to form bone mineral crystals, limit current analyses of labile diffusible, amorphous, and crystalline intermediates by electron microscopy. To improve the retention of calcium and phosphorus, we developed a pseudo nonaqueous processing approach and used it to characterize biomineralization foci, extracellular sites of hydroxyapatite deposition in osteoblastic cell cultures. Since mineralization of UMR106-01 osteoblasts is temporally synchronized and begins 78 h after plating, we used these cultures to evaluate the effectiveness of our method when applied to cells just prior to the formation of the first mineral crystals. Our approach combines for the first time 3 well-established methods with a fourth one, i.e. dry ultrathin sectioning. Dry ultrathin sectioning with an oscillating diamond knife was used to produce electron spectroscopic images of mineralized biomineralization foci which were high-pressure frozen and freeze substituted. For comparison, cultures were also treated with conventional processing and wet sectioning. The results show that only the use of pseudo nonaqueous processing was able to detect extracellular sites of early calcium and phosphorus enrichment at 76 h, several hours prior to detection of mineral crystals within biomineralization foci.

Fossil versus contemporary sources of fine elemental and organic carbonaceous particulate matter during the DAURE campaign in Northeast Spain

We present results from the international field campaign DAURE (Detn. of the sources of atm. Aerosols in Urban and Rural Environments in the Western Mediterranean), with the objective of apportioning the sources of fine carbonaceous aerosols. Submicron fine particulate matter (PM1) samples were collected during Feb.-March 2009 and July 2009 at an urban background site in Barcelona (BCN) and at a forested regional background site in Montseny (MSY). We present radiocarbon (14C) anal. for elemental and org. carbon (EC and OC) and source apportionment for these data. We combine the results with those from component anal. of aerosol mass spectrometer (AMS) measurements, and compare to levoglucosan-based ests. of biomass burning OC, source apportionment of filter data with inorg. compn. + EC + OC, submicron bulk potassium (K) concns., and gaseous acetonitrile concns. At BCN, 87 % and 91 % of the EC on av., in winter and summer, resp., had a fossil origin, whereas at MSY these fractions were 66 % and 79 %. The contribution of fossil sources to org. carbon (OC) at BCN was 40 % and 48 %, in winter and summer, resp., and 31 % and 25 % at MSY. The combination of results obtained using the 14C technique, AMS data, and the correlations between fossil OC and fossil EC imply that the fossil OC at Barcelona is ∼47 % primary whereas at MSY the fossil OC is mainly secondary (∼85 %). Day-to-day variation in total carbonaceous aerosol loading and the relative contributions of different sources predominantly depended on the meteorol. transport conditions. The estd. biogenic secondary OC at MSY only increased by ∼40 % compared to the order-of-magnitude increase obsd. for biogenic volatile org. compds. (VOCs) between winter and summer, which highlights the uncertainties in the estn. of that component. Biomass burning contributions estd. using the 14C technique ranged from similar to slightly higher than when estd. using other techniques, and the different estns. were highly or moderately correlated. Differences can be explained by the contribution of secondary org. matter (not included in the primary biomass burning source ests.), and/or by an over-estn. of the biomass burning OC contribution by the 14C technique if the estd. biomass burning EC/OC ratio used for the calcns. is too high for this region. Acetonitrile concns. correlate well with the biomass burning EC detd. by 14C. K is a noisy tracer for biomass burning. [on SciFinder(R)]