In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new ...segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website http://tubic.tju.edu.cn/GC-Profile/. In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.
Disease detection through gas analysis has long been the topic of many studies because of its potential as a rapid diagnostic technique. In particular, the pathogens that cause urinary tract ...infection (UTI) have been shown to generate different profiles of volatile organic compounds, thus enabling the discrimination of causative agents using an electronic nose. While past studies have performed data collection on either agar culture or jellified urine culture, this study measures the headspace volume of liquid urine culture samples. Evaporation of the liquid and the presence of background compounds during electronic nose (e-nose) device operation could introduce variability to the collected data. Therefore, a headspace gas chromatography-mass spectrometry method was developed and validated for quantitating ethanol in the headspace of the urine samples. By leveraging the new method to characterize the sample stability during e-nose measurement, it was revealed that ethanol concentration dropped more than 15% after only three measurement cycles, which equal 30 minutes for this study. It was further shown that by using only data within the first three cycles, better accuracies for between-day classification were achieved, which was 73.7% and 97.0%, compared to using data from within the first nine cycles, which resulted in 65.0% and 81.1% accuracies. Therefore, the newly developed method provides better quality control for data collection, paving ways for the future establishment of a training data library for UTI.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
2-Methiopropamine 1-(thiophen-2-yl)-2-methylaminopropane, 2-MPA, a thiophene analogue of methamphetamine, is available from online vendors selling “research chemicals.” The first samples were seized ...by the German police in 2011. As it is a recreational stimulant, its inclusion in routine drug screening protocols should be required. The aims of this study were to identify the phase I and II metabolites of 2-MPA in rat and human urine and to identify the human cytochrome-P450 (CYP) isoenzymes involved in its phase I metabolism. In addition, the detectability of 2-MPA in urine samples using the authors’ well-established gas chromatography–mass spectrometry (GC-MS) and liquid chromatography-linear ion trap-mass spectrometry (LC-MS
n
) screening protocols was also evaluated. The metabolites were isolated from rat and human urine samples by solid-phase extraction without or following enzymatic cleavage of conjugates. The phase I metabolites, following acetylation, were separated and identified by GC-MS and/or liquid chromatography–high-resolution linear ion trap mass spectrometry (LC-HR-MS
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) and the phase II metabolites by LC-HR-MS
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. The following major metabolic pathways were proposed:
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-demethylation, hydroxylation at the side chain and at the thiophene ring, and combination of these transformations followed by glucuronidation and/or sulfation. CYP1A2, CYP2C19, CYP2D6, and CYP3A4 were identified as the major phase I metabolizing enzymes. They were also involved in the
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-demethylation of the analogue methamphetamine and CYP2C19, CYP2D6, and CYP3A4 in its ring hydroxylation. Following the administration of a typical user’s dose, 2-MPA and its metabolites were identified in rat urine using the authors’ GC-MS and the LC-MS
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screening approaches. Ingestion of 2-MPA could also be detected by both protocols in an authentic human urine sample.
Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of ...online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis.
Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline.
MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The purpose of this study was to determine the concentrations of mineral oil hydrocarbons in dry foodstuffs packed in recycled paperboard, which were imported from different foreign countries to ...Germany. After collection, mineral oil saturated hydrocarbons (MOSH) and mineral oil aromatic hydrocarbons (MOAH) in dry foodstuffs and recycled paperboard were analysed using online coupled high-performance liquid chromatography-gas chromatography-flame ionisation detection (online HPLC-GC-FID) far before the end of the shelf life of the samples. Our results showed that recycled paperboard has MOAH content higher than that of dry foodstuffs. The proportion of MOAH within total mineral oil hydrocarbons was determined to be 7-45% in dry foodstuffs and 4-48% in paperboard. In addition, 29% of the products were found to contain over 1.00 mg/kg MOAH, with a maximum of 2.72 mg/kg in oatmeal. White colour recycled paperboard contained lower amounts of MOSH and MOAH than that of brown and grey colour recycled paperboard. The MOSH concentration in dry foodstuffs ranged from 0.11 to 21.92 mg/kg (˂C25 hydrocarbons), which may be an indication of rapid migration. The lowest determined MOSH concentrations (˂C25 hydrocarbons) were found in sea salt and soda samples, even when their paperboard contained high mineral oil hydrocarbons. Our three samples in packages containing internal bags (for complete barriers) were found to have low mineral oil concentration due to reduced migration through plastic (acrylate-coated polypropylene). However, one sample, a 'crispy' product with an internal bag, contained the extreme amount of 21.92 mg/kg. Differences in contaminants observed in both dry foodstuffs and recycled paperboard may have been due to the different packaging and production techniques of the different countries. In addition, 8 of 24 dry foodstuff samples contained MOSH concentrations frequently exceeding the 2.0 mg/kg limit for MOSH C
20
-C
35
.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The authors report the case of a 41-year-old man known as a polydrug addict and found dead at home. The initial toxicological screening was inconclusive for a toxic death. However, 7 small bags of ...unknown powders and crystals, supposed to be NPS, were found near the body and sent to the laboratory 3 weeks later. This article focuses on the interest of nuclear magnetic resonance (NMR) spectroscopy to solve this fatal case. The 7 items were identified by
H NMR and their purities were measured by the quantitative NMR (qNMR) method using maleic acid as internal standard. The compounds were 4-chloro-α-pyrrolidinopentiophenone, dibutylone, 4-chloroethcathinone, 4-α-pyrrolidinohexuiphenone, 3,4-methylenedioxy-N-benzylcathinone, 3-methoxy-phencyclidine and α-pyrrolidinopropiophenone, with purities in the range 51-89%. In the biological specimens of the victim, only 3-methoxy-phencyclidine (3-MeO-PCP) was identified in cardiac blood, peripheral blood and urine at 743, 489 and 16,700 ng/mL. Hair (6 cm) concentration of the drug was 15,600 pg/mg. The other NPS were not detected. The peripheral blood concentration was higher than the values reported in previous intoxicated and fatal cases. The toxicological significance of the measured concentration in hair was difficult to establish because this is only the second case describing a test result for 3-MeO-PCP.
SIMAT: GC-SIM-MS data analysis tool Ranjbar, Mohammad R Nezami; Di Poto, Cristina; Wang, Yue ...
BMC bioinformatics,
08/2015, Letnik:
16, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single ...quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, there are no software tools specifically designed for analysis of GC-SIM-MS data. In this paper, we introduce a new R/Bioconductor package called SIMAT for quantitative analysis of the levels of targeted analytes. SIMAT provides guidance in choosing fragments for a list of targets. This is accomplished through an optimization algorithm that has the capability to select the most appropriate fragments from overlapping chromatographic peaks based on a pre-specified library of background analytes. The tool also allows visualization of the total ion chromatograms (TIC) of runs and extracted ion chromatograms (EIC) of analytes of interest. Moreover, retention index (RI) calibration can be performed and raw GC-SIM-MS data can be imported in netCDF or NIST mass spectral library (MSL) formats.
We evaluated the performance of SIMAT using two GC-SIM-MS datasets obtained by targeted analysis of: (1) plasma samples from 86 patients in a targeted metabolomic experiment; and (2) mixtures of internal standards spiked in plasma samples at varying concentrations in a method development study. Our results demonstrate that SIMAT offers alternative solutions to AMDIS and MetaboliteDetector to achieve accurate detection of targets and estimation of their relative intensities by analysis of GC-SIM-MS data.
We introduce a new R package called SIMAT that allows the selection of the optimal set of fragments and retention time windows for target analytes in GC-SIM-MS based analysis. Also, various functions and algorithms are implemented in the tool to: (1) read and import raw data and spectral libraries; (2) perform GC-SIM-MS data preprocessing; and (3) plot and visualize EICs and TICs.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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