XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

Tautenhahn, Ralf; Patti, Gary J.; Rinehart, Duane; Siuzdak, Gary

doi:10.1021/ac300698c

Cited by 1,141 publications

(899 citation statements)

References 27 publications

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“…Raw data files obtained from LC‐MS experiments were converted to the mzData format using Agilent Masshunter software, grouped into directories by population, and then uploaded to the XCMS Online platform (Tautenhahn, Patti, Rinehart, & Siuzdak, 2012) for automatic metabolite detection and alignment. Metabolite features—peaks defined by mass‐to‐charge ratio (m/z), retention time (RT), and intensity—were extracted with optimized parameters: centWave method, minimum–maximum peak width = 8 and 30, signal‐to‐noise threshold = 30, mzdiff = 0.01, prefilter peaks = 3, prefilter intensity = 2,000, and noise filter = 0.…”

Section: Methodsmentioning

confidence: 99%

“…A preliminary PCA using autoscaled distances of individual peak areas and a distance to model (DModX) test (implemented in XCMS) detected individual UM19 as a significant outlier sample (possibly due to extraction error) to be removed. As one metabolite may give rise to multiple peaks including isotope, adduct, or fragment peaks, the 2,785 peaks were further grouped by peak intensity correlation and RT similarity using built‐in procedures from the XCMS pipeline (Tautenhahn et al., 2012). This resulted in 377 metabolites, which were represented by the largest peak within each group.…”

Section: Methodsmentioning

confidence: 99%

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Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.

Pais

Xiang

2018

Ecology and Evolution

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Understanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment‐driven plasticity. Next‐generation sequencing, untargeted liquid chromatography–mass spectrometry (LC‐MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease‐threatened Cornus florida L. from distinct ecological regions using genotype‐by‐sequencing markers and LC‐MS‐based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity in C. florida yielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied‐allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.

Pais

Xiang

2018

Ecology and Evolution

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“…Peak identification used the NIST 2005 Mass Spectra Library V2.1. Chromatographic data was processed using XCMS Online from the Scripps Center for Metabolomics 26. Linear Discriminant Analysis was carried out using IBM SPSS Statistics 22.…”

Section: Methodsmentioning

confidence: 99%

Classifying Degraded Modern Polymeric Museum Artefacts by Their Smell

et al. 2018

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The use of VOC analysis to diagnose degradation in modern polymeric museum artefacts is reported. Volatile organic compound (VOC) analysis is a successful method for diagnosing medical conditions but to date has found little application in museums. Modern polymers are increasingly found in museum collections but pose serious conservation difficulties owing to unstable and widely varying formulations. Solid‐phase microextraction gas chromatography/mass spectrometry and linear discriminant analysis were used to classify samples according to the length of time they had been artificially degraded. Accuracies in classification of 50–83 % were obtained after validation with separate test sets. The method was applied to three artefacts from collections at Tate to detect evidence of degradation. This approach could be used for any material in heritage collections and more widely in the field of polymer degradation.

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“…All solvents contained 0.1% formic acid. Total ion chromatograms were analyzed with XCMS software (45) available online at the Scripps Center for Metabolomics (93).…”

Section: Methodsmentioning

confidence: 99%

Two-photon microscopy reveals early rod photoreceptor cell damage in light-exposed mutant mice

Maeda

Palczewska

Golczak³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Atrophic age-related and juvenile macular degeneration are especially devastating due to lack of an effective cure. Two retinal cell types, photoreceptor cells and the adjacent retinal pigmented epithelium (RPE), reportedly display the earliest pathological changes. Abca4 −/− Rdh8 −/− mice, which mimic many features of human retinal degeneration, allowed us to determine the sequence of light-induced events leading to retinal degeneration. Using two-photon microscopy with 3D reconstruction methodology, we observed an initial strong retinoid-derived fluorescence and expansion of Abca4 −/− Rdh8 −/− mouse rod cell outer segments accompanied by macrophage infiltration after brief exposure of the retina to bright light. Additionally, light-dependent fluorescent compounds produced in rod outer segments were not transferred to the RPE of mice genetically defective in RPE phagocytosis. Collectively, these findings suggest that for light-induced retinopathies in mice, rod photoreceptors are the primary site of toxic retinoid accumulation and degeneration, followed by secondary changes in the RPE.

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XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

Cited by 1,141 publications

References 27 publications

Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.

Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.

Classifying Degraded Modern Polymeric Museum Artefacts by Their Smell

Two-photon microscopy reveals early rod photoreceptor cell damage in light-exposed mutant mice

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