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

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

2012 June 5 | Ralf Tautenhahn, Gary J. Patti, Duane Rinehart, and Gary Siuzdak
XCMS Online is a web-based platform for processing untargeted metabolomic data, designed to be user-friendly and accessible to non-bioinformaticians. It allows users to upload and process liquid chromatography/mass spectrometry (LC/MS) data with minimal technical expertise. The platform provides a complete workflow for untargeted metabolomics, including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be viewed online in an interactive table, and all results and images can be downloaded for offline analysis and publication. Untargeted metabolomics involves the global profiling of small molecules in a biological system without bias. LC/MS is commonly used due to its ability to measure a large number of metabolites simultaneously. However, the complexity of the data makes manual comparison impractical, and retention time drifts can complicate interpretation. Automated data processing, such as retention time alignment, is essential. Several software programs exist for processing LC/MS-based metabolomic data, but they often require technical expertise or have proprietary restrictions. XCMS Online addresses these limitations by providing a web-based solution that requires no installation or technical expertise. It is based on the widely used XCMS software, which has been used in various applications, including cancer research, chronic pain, and stem cell differentiation. XCMS Online processes data in three steps: data upload, parameter selection, and result interpretation. Users can upload files in formats such as netCDF, mzXML, mzData, and Agilent .d folders. Files are compressed and encrypted before upload. Users can select predefined or customized parameter sets for their instrument setup. Data processing can take several minutes to several hours, and multiple jobs can be submitted simultaneously. Results are visualized through various plots, including mirror plots, multidimensional scaling (MDS), and principal component analysis (PCA) plots. These plots help in identifying dysregulated features and assessing data quality. The feature table browser provides detailed information for each feature, including statistics, extracted ion chromatograms, and putative METLIN identifications. Users can filter results based on various criteria, such as p-value, fold change, and intensity. XCMS Online is a valuable tool for researchers without bioinformatic expertise, providing a complete solution for untargeted metabolomic analysis. It facilitates data interpretation and prioritization, making it accessible for a broader scientific community.XCMS Online is a web-based platform for processing untargeted metabolomic data, designed to be user-friendly and accessible to non-bioinformaticians. It allows users to upload and process liquid chromatography/mass spectrometry (LC/MS) data with minimal technical expertise. The platform provides a complete workflow for untargeted metabolomics, including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be viewed online in an interactive table, and all results and images can be downloaded for offline analysis and publication. Untargeted metabolomics involves the global profiling of small molecules in a biological system without bias. LC/MS is commonly used due to its ability to measure a large number of metabolites simultaneously. However, the complexity of the data makes manual comparison impractical, and retention time drifts can complicate interpretation. Automated data processing, such as retention time alignment, is essential. Several software programs exist for processing LC/MS-based metabolomic data, but they often require technical expertise or have proprietary restrictions. XCMS Online addresses these limitations by providing a web-based solution that requires no installation or technical expertise. It is based on the widely used XCMS software, which has been used in various applications, including cancer research, chronic pain, and stem cell differentiation. XCMS Online processes data in three steps: data upload, parameter selection, and result interpretation. Users can upload files in formats such as netCDF, mzXML, mzData, and Agilent .d folders. Files are compressed and encrypted before upload. Users can select predefined or customized parameter sets for their instrument setup. Data processing can take several minutes to several hours, and multiple jobs can be submitted simultaneously. Results are visualized through various plots, including mirror plots, multidimensional scaling (MDS), and principal component analysis (PCA) plots. These plots help in identifying dysregulated features and assessing data quality. The feature table browser provides detailed information for each feature, including statistics, extracted ion chromatograms, and putative METLIN identifications. Users can filter results based on various criteria, such as p-value, fold change, and intensity. XCMS Online is a valuable tool for researchers without bioinformatic expertise, providing a complete solution for untargeted metabolomic analysis. It facilitates data interpretation and prioritization, making it accessible for a broader scientific community.
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