Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0239-3_17
Abstract: MetaboAnalyst ( www.metaboanalyst.ca ) is an easy-to-use, comprehensive web-based tool, freely available for metabolomics data processing, statistical analysis, functional interpretation, as well as integration with other omics data. This chapter first provides an introductory overview… read more here.
Keywords: metabolomics data; metaboanalyst; analysis; omics data ... See more keywords
Metabolomics Data Processing Using XCMS.
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DOI: 10.1007/978-1-0716-0239-3_2
Abstract: XCMS is one of the most used software for liquid chromatography-mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter,… read more here.
Keywords: metabolomics data; data processing; processing using; using xcms ... See more keywords
A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics
Sign Up to like & getrecommendations! Published in 2019 at "Metabolomics"
DOI: 10.1007/s11306-019-1564-8
Abstract: We previously developed a tandem mass spectrometry-based label-free targeted metabolomics analysis framework coupled to two distinct chromatographic methods, reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC), with dynamic multiple reaction monitoring (dMRM) for… read more here.
Keywords: large scale; metabolomics data; analysis; targeted metabolomics ... See more keywords
Processing of NMR and MS metabolomics data using chemometrics methods: a global tool for fungi biotransformation reactions monitoring
Sign Up to like & getrecommendations! Published in 2019 at "Metabolomics"
DOI: 10.1007/s11306-019-1567-5
Abstract: Biotransformation constitutes an important aspect of the drug discovery process, to mimic human metabolism of active principal ingredient but also to generate new chemical entities. Several microorganisms such as fungi are well adapted to transform… read more here.
Keywords: metabolomics data; production; processing nmr; biotransformation ... See more keywords
A comparative evaluation of the generalised predictive ability of eight machine learning algorithms across ten clinical metabolomics data sets for binary classification
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DOI: 10.1007/s11306-019-1612-4
Abstract: Metabolomics is increasingly being used in the clinical setting for disease diagnosis, prognosis and risk prediction. Machine learning algorithms are particularly important in the construction of multivariate metabolite prediction. Historically, partial least squares (PLS) regression… read more here.
Keywords: machine; metabolomics data; machine learning; generalised predictive ... See more keywords
Statistical reporting of metabolomics data: experience from a high-throughput NMR platform and epidemiological applications
Sign Up to like & getrecommendations! Published in 2019 at "Metabolomics"
DOI: 10.1007/s11306-019-1626-y
Abstract: Meta-analysis is the cornerstone of robust biomedical evidence. We investigated whether statistical reporting practices facilitate metabolomics meta-analyses. A literature review of 44 studies that used a comparable platform. Non-numeric formats were used in 31 studies.… read more here.
Keywords: metabolomics data; reporting metabolomics; data experience; experience high ... See more keywords
Paramounter: Direct Measurement of Universal Parameters To Process Metabolomics Data in a "White Box".
Sign Up to like & getrecommendations! Published in 2022 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.1c04758
Abstract: Choosing appropriate data processing parameters is critical in processing liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics data. The conventional design of experiments (DOE) approach is time-consuming and provides no intuitive explanation why the selected parameters generate… read more here.
Keywords: paramounter; feature extraction; universal parameters; metabolomics data ... See more keywords
Biologically Consistent Annotation of Metabolomics Data.
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DOI: 10.1021/acs.analchem.7b02162
Abstract: Annotation of metabolites remains a major challenge in liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics. The current gold standard for metabolite identification is to match the detected feature with an authentic standard analyzed on the… read more here.
Keywords: metabolomics data; consistent annotation; annotation metabolomics; annotation ... See more keywords
Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey
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DOI: 10.1038/s41598-021-01652-1
Abstract: REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) is a global strategy and regulation policy of the EU that aims to improve the protection of human health and the environment through the better and earlier… read more here.
Keywords: quality; metabolomics data; analysis; toxicity ... See more keywords
Inference of cancer mechanisms through computational systems analysis.
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DOI: 10.1039/c6mb00672h
Abstract: Large amounts of metabolomics data have been accumulated to study metabolic alterations in cancer that allow cancer cells to synthesize molecular materials necessary for cell growth and proliferation. Although metabolic reprogramming in cancer was discovered… read more here.
Keywords: metabolomics data; analysis; method; inference cancer ... See more keywords
TIGER: technical variation elimination for metabolomics data using ensemble learning architecture
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DOI: 10.1093/bib/bbab535
Abstract: Abstract Large metabolomics datasets inevitably contain unwanted technical variations which can obscure meaningful biological signals and affect how this information is applied to personalized healthcare. Many methods have been developed to handle unwanted variations. However,… read more here.
Keywords: ensemble learning; metabolomics data; learning architecture; tiger technical ... See more keywords