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

By Ralf Tautenhahn, G. Patti, Duane Rinehart, Gary Siuzdak. Analytical Chemistry, 2012

1,189 citations recorded by the source corpus.

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 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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/449e358c5aa84c04d78f1898184c41153f15fc6a

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Citations in the corpus

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, methodology): “The XCMS Online platform has partially addressed the issue by offering several pre-optimized platform-specific parameters (10,33).”
IPO: a tool for automated optimization of XCMS parameters (2015, methodology): “A number of software packages for processing LC-MS data have already been developed for data sets of samples that do not rely on labeling [3-12].”
Analytical Methods in Untargeted Metabolomics: State of the Art in 2015 (2015, positive): “This type of method is implemented in the XCMS software (Tautenhahn et al., 2012b), one of the most commonly used methods to process data from LC-MS studies.”
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis (2019, methodology): “Outside of MetaboAnalyst, there are several other freely available web-based metabolomic data processing tools—MeltDB (Kessler et al., 2013), MetabolomeExpress (Carroll, Badger, & Harvey Millar, 2010), and XCMS Online (Huan et al., 2017; Tautenhahn et al., 2012).”
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation (2024, methodology): “Table 1 compares the main features of MetaboAnalyst 6.0 with other popular tools including the previous version, XCMS online ( 23 ), GNPS ( 45 ), Workflow4Metabolomics (W4M) ( 67 ) and MetExplore ( 68 ).”
Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics (2014, background): “Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure.”
Computational mass spectrometry for small molecules (2013, methodology): “XCMS Online [243] is the web-based version of the software.”
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis (2016, methodology): “In particular, MeltDB and MetabolomeExpress have Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis 14.10.88 Supplement 55 Current Protocols in Bioinformatics been primarily developed for MS-based metabolomics data storage, administration, analysis, and annotation; XCMS Online is a”