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Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G - Anal. Chem. (2014)

Bottom Line: On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity.The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots.The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria.

View Article: PubMed Central - PubMed

Affiliation: Scripps Center for Metabolomics and Mass Spectrometry and ‡Department of Cell Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

ABSTRACT
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.

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Related in: MedlinePlus

Interactive cloud plot with customized metabolomicdata visualization.When a user scrolls the mouse over a bubble, feature assignments aredisplayed in a pop-up window (m/z, RT, p-value, fold change) with potential METLINhits. Each bubble is linked to the METLIN database to provide putativeidentifications based on accurate m/z. When a bubble is selected by a mouse click, its EIC, box–whiskerplot, and MS spectrum appear on the bottom of the main panel. Thefeature with m/z 694.458 and a putativeMETLIN hit for glycerophosphoserine (PS) seems to be specific to theSUP-T1 parental cell line.
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fig4: Interactive cloud plot with customized metabolomicdata visualization.When a user scrolls the mouse over a bubble, feature assignments aredisplayed in a pop-up window (m/z, RT, p-value, fold change) with potential METLINhits. Each bubble is linked to the METLIN database to provide putativeidentifications based on accurate m/z. When a bubble is selected by a mouse click, its EIC, box–whiskerplot, and MS spectrum appear on the bottom of the main panel. Thefeature with m/z 694.458 and a putativeMETLIN hit for glycerophosphoserine (PS) seems to be specific to theSUP-T1 parental cell line.

Mentions: A typical untargeted metabolomicexperiment comparing any two conditions(e.g., normal vs disease) yields hundreds of altered features. Tovisualize the results and filter out significantly altered features,the original cloud plot18 has been expandedfrom simply providing feature assignments (m/z, retention time, p-value, and directionalfold change) to the interactive cloud plot or a dynamic interfaceenabling users to customize the display (Figure 3 and 4). The default view shows a “mainpanel” that allows users to modify p-valueand fold-change filters (Figure 3), where thethresholds can be changed either by using a slider or the text boxbelow the slider. An “advanced” selection panel allowsusers to modify m/z range, retentiontime, and ion-intensity range, depending on the features of interest.Additional choices provided in the advanced selection panel includemultiple color options for up-regulated and down-regulated metabolicfeatures, options to enable or disable TICs, colorize TICs, mark featureswith METLIN hits19 and also to either showor hide isotopic peaks. Furthermore, the “zoom” functionalityallows users to focus and magnify a desired area of the plot by draggingthe cursor across that area. This functionality is useful in plotswith large numbers of data points that cluster together. The plotcan be reset to the original view with a “mouse click”.


Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G - Anal. Chem. (2014)

Interactive cloud plot with customized metabolomicdata visualization.When a user scrolls the mouse over a bubble, feature assignments aredisplayed in a pop-up window (m/z, RT, p-value, fold change) with potential METLINhits. Each bubble is linked to the METLIN database to provide putativeidentifications based on accurate m/z. When a bubble is selected by a mouse click, its EIC, box–whiskerplot, and MS spectrum appear on the bottom of the main panel. Thefeature with m/z 694.458 and a putativeMETLIN hit for glycerophosphoserine (PS) seems to be specific to theSUP-T1 parental cell line.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215863&req=5

fig4: Interactive cloud plot with customized metabolomicdata visualization.When a user scrolls the mouse over a bubble, feature assignments aredisplayed in a pop-up window (m/z, RT, p-value, fold change) with potential METLINhits. Each bubble is linked to the METLIN database to provide putativeidentifications based on accurate m/z. When a bubble is selected by a mouse click, its EIC, box–whiskerplot, and MS spectrum appear on the bottom of the main panel. Thefeature with m/z 694.458 and a putativeMETLIN hit for glycerophosphoserine (PS) seems to be specific to theSUP-T1 parental cell line.
Mentions: A typical untargeted metabolomicexperiment comparing any two conditions(e.g., normal vs disease) yields hundreds of altered features. Tovisualize the results and filter out significantly altered features,the original cloud plot18 has been expandedfrom simply providing feature assignments (m/z, retention time, p-value, and directionalfold change) to the interactive cloud plot or a dynamic interfaceenabling users to customize the display (Figure 3 and 4). The default view shows a “mainpanel” that allows users to modify p-valueand fold-change filters (Figure 3), where thethresholds can be changed either by using a slider or the text boxbelow the slider. An “advanced” selection panel allowsusers to modify m/z range, retentiontime, and ion-intensity range, depending on the features of interest.Additional choices provided in the advanced selection panel includemultiple color options for up-regulated and down-regulated metabolicfeatures, options to enable or disable TICs, colorize TICs, mark featureswith METLIN hits19 and also to either showor hide isotopic peaks. Furthermore, the “zoom” functionalityallows users to focus and magnify a desired area of the plot by draggingthe cursor across that area. This functionality is useful in plotswith large numbers of data points that cluster together. The plotcan be reset to the original view with a “mouse click”.

Bottom Line: On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity.The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots.The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria.

View Article: PubMed Central - PubMed

Affiliation: Scripps Center for Metabolomics and Mass Spectrometry and ‡Department of Cell Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

ABSTRACT
XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, "control" versus "disease" experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.

Show MeSH
Related in: MedlinePlus