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. 2012 Jun 5;84(11):5035-9.
doi: 10.1021/ac300698c. Epub 2012 May 10.

XCMS Online: a web-based platform to process untargeted metabolomic data

Ralf Tautenhahn  1 , Gary J Patti, Duane Rinehart, Gary Siuzdak
Affiliations

XCMS Online: a web-based platform to process untargeted metabolomic data

Ralf Tautenhahn et al. Anal Chem. .

Abstract

Recently, interest in untargeted metabolomics has become prevalent in the general scientific community among an increasing number of investigators. The majority of these investigators, however, do not have the bioinformatic expertise that has been required to process metabolomic data by using command-line driven software programs. Here we introduce a novel platform to process untargeted metabolomic data that uses an intuitive graphical interface and does not require installation or technical expertise. This platform, called XCMS Online, is a web-based version of the widely used XCMS software that allows users to easily upload and process liquid chromatography/mass spectrometry data with only a few mouse clicks. XCMS Online provides a solution for the complete untargeted metabolomic workflow including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be browsed online in an interactive, customizable table showing statistics, chromatograms, and putative METLIN identities for each metabolite. Additionally, all results and images can be downloaded as zip files for offline analysis and publication. XCMS Online is available at https://xcmsonline.scripps.edu.

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Figures

Figure 1
Figure 1
XCMS Online workflow: LC/MS-based metabolomic data is processed in three simple steps.
Figure 2
Figure 2
XCMS Online screen shot showing the overview of results from an untargeted analysis. The top display panels includes text on general job information such dataset names, parameter set names, and job date. The lower display panels are used toprovide a global visualization of the experimental results (labeled d-f) in addition to plots that can be used for quality control(labeled a-c,e,f). The display shows the overlay of total ion chromatograms before (a) and after (c) retention time correction; theretention time correction curve (b); mirror plot (d); multidimensional scaling (e), and principal component analysis (f). Colorcodings: Samples are color coded in a-c, the same color mapping is used for the samples across these 3 figures. In the mirror plot (d)upregulated features are shown in green, downregulated features in red. For the PCA and MDS plot (e,f) colors are used to highlightthe different sample classes (here red for control group and blue for disease model).
Figure 3
Figure 3
XCMS Online screen shot showing the feature browser that is used to display detailed information for eachindividual feature including statistics (a), extracted ion chromatograms (b), spectrum details (c), and putative METLINidentifications (d).
See this image and copyright information in PMC

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