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

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

doi:10.1021/ac300698c

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

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.

Authors:

Tautenhahn, Ralf ^[1]; Patti, Gary J. ^[2]; Rinehart, Duane ^[1]; Siuzdak, Gary ^[1]

The Scripps Research Inst., La Jolla, CA (United States). Center for Metabolomics, Dept. of Chemistry and Molecular Biology
Washington Univ., St. Louis, MO (United States). Depts. of Chemistry, Genetics, and Medicine

Publication Date:: Tue Jun 05 00:00:00 EDT 2012

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1788449

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Analytical Chemistry

Additional Journal Information:: Journal Volume: 84; Journal Issue: 11; Journal ID: ISSN 0003-2700

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats


                    Tautenhahn, Ralf, Patti, Gary J., Rinehart, Duane, and Siuzdak, Gary. XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data.  United States: N. p., 2012. 
Web.  doi:10.1021/ac300698c.

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                    Tautenhahn, Ralf, Patti, Gary J., Rinehart, Duane, & Siuzdak, Gary. XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data.  United States.  https://doi.org/10.1021/ac300698c

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                    Tautenhahn, Ralf, Patti, Gary J., Rinehart, Duane, and Siuzdak, Gary. Tue .  
"XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data".  United States.  https://doi.org/10.1021/ac300698c.  https://www.osti.gov/servlets/purl/1788449.

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@article{osti_1788449,

  title        = {XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data},

  author       = {Tautenhahn, Ralf and Patti, Gary J. and Rinehart, Duane and Siuzdak, Gary},

  abstractNote = {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.},

  doi          = {10.1021/ac300698c},

  journal      = {Analytical Chemistry},

  number       = 11,

  volume       = 84,

  place        = {United States},

  year         = {Tue Jun 05 00:00:00 EDT 2012},

  month        = {Tue Jun 05 00:00:00 EDT 2012}

}

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Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses

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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 metabolicmore »« less
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Computational metabolite annotation in untargeted profiling aims at uncovering neutral molecular masses of underlying metabolites and assign those with putative identities. Existing annotation strategies rely on the observation and annotation of adducts to determine metabolite neutral masses. However, a significant fraction of features usually detected in untargeted experiments remains unannotated, which limits our ability to determine neutral molecular masses. Despite the availability of tools to annotate, relatively few of them benefit from the inherent presence of in-source fragments in liquid chromatography-electrospray ionization-mass spectrometry. Here, we introduce a strategy to annotate in-source fragments in untargeted data using low-energy tandem mass spectrometrymore »« less
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Identification of volatile markers for the detection of adulterants in red ginseng ( Panax ginseng ) juice using headspace stir-bar sorptive extraction coupled with gas chromatography and mass spectrometry journal, July 2018

Proteomics analysis of tumor microenvironment: Implications of metabolic and oxidative stresses in tumorigenesis: PROTEOMICS ANALYSIS OF TUMOR MICROENVIRONMENT journal, November 2012

Metabolomics toward personalized medicine journal, October 2017

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation journal, November 2017

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies journal, October 2018

Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase: Novel Resorcylic Acid by Stilbene Synthase Mutant journal, December 2014

Combined maternal and post‐weaning high fat diet inhibits male offspring's prostate cancer tumorigenesis in transgenic adenocarcinoma of mouse prostate model journal, December 2018

Principal component analysis of normalized full spectrum mass spectrometry data in multiMS-toolbox: An effective tool to identify important factors for classification of different metabolic patterns and bacterial strains journal, May 2018

Retention time shift analysis and correction in chemical isotope labeling liquid chromatography/mass spectrometry for metabolome analysis journal, April 2020

Quantitative determination of major platelet activating factors from human plasma journal, March 2014

Evaluation of changes induced in rice metabolome by Cd and Cu exposure using LC-MS with XCMS and MCR-ALS data analysis strategies journal, September 2015

Novel analytical methods to study the fate of mycotoxins during thermal food processing journal, October 2019

Promises and pitfalls of untargeted metabolomics journal, March 2018

Global metabolomics reveals metabolic dysregulation in ischemic retinopathy journal, November 2015

Matrix binding of T-2 toxin: structure elucidation of reaction products and indications on the fate of a relevant food-borne toxin during heating journal, March 2019

Personal genomes, quantitative dynamic omics and personalized medicine journal, January 2013

The WEIZMASS spectral library for high-confidence metabolite identification journal, August 2016

Revealing disease-associated pathways by network integration of untargeted metabolomics journal, August 2016

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database journal, February 2013

The re-emergence of natural products for drug discovery in the genomics era journal, January 2015

The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation journal, November 2017

The microbiota regulate neuronal function and fear extinction learning journal, October 2019

Mass spectrometry searches using MASST journal, January 2020

Systems-level analysis of isotopic labeling in untargeted metabolomic data by X13CMS journal, June 2019

Separation of blood microsamples by exploiting sedimentation at the microscale journal, September 2018

Defining Dysbiosis in Patients with Urolithiasis journal, April 2019

Starvation-induced collective behavior in C. elegans journal, May 2015

Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis journal, August 2015

Metabolomic analysis with GC-MS to reveal potential metabolites and biological pathways involved in Pb & Cd stress response of radish roots journal, December 2015

Citrate Accumulation-Related Gene Expression and/or Enzyme Activity Analysis Combined With Metabolomics Provide a Novel Insight for an Orange Mutant journal, July 2016

A global approach to analysis and interpretation of metabolic data for plant natural product discovery journal, January 2013

Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products journal, January 2014

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites journal, January 2017

Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples journal, January 2019

Metabolic profile analysis of Zhi-zi-chi decoction in feces of normal and chronic unpredictable mild stress-induced depression rats based on UHPLC-ESI-Q-TOF-MS/MS and multiple analytical strategies journal, January 2019

Onchocerca volvulus -neurotransmitter tyramine is a biomarker for river blindness journal, February 2013

Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria journal, June 2017

Beyond monoisotopic accurate mass spectrometry: ancillary techniques for identifying unknown features in non-targeted discovery analysis journal, November 2018

Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis journal, September 2015

Low-cost microphysiological systems: Feasibility study of a tape-based barrier-on-chip system for small intestine modeling posted_content, January 2020

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS posted_content, January 2020

Drying enhances signal intensity for global GC-MS metabolomics posted_content, January 2019

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data posted_content, March 2019

Intestinal peroxisomal fatty acid β-oxidation regulates neural serotonin signaling through a feedback mechanism posted_content, January 2019

Piezo1 Induces Local Curvature in a Mammalian Membrane and Forms Specific Protein-Lipid Interactions posted_content, January 2019

Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin
journal, January 2012

Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping
journal, September 2006

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets
journal, December 2011

Redirection of Flavonoid Biosynthesis through the Down-Regulation of an Anthocyanidin Glucosyltransferase in Ripening Strawberry Fruit
journal, February 2008

A direct approach to false discovery rates
journal, August 2002

MetaboAnalyst: a web server for metabolomic data analysis and interpretation
journal, May 2009

MetAlign: Interface-Driven, Versatile Metabolomics Tool for Hyphenated Full-Scan Mass Spectrometry Data Preprocessing
journal, March 2009

meta P- Server : A Web-Based Metabolomics Data Analysis Tool
journal, January 2011

Metabonomics study of liver cancer based on ultra performance liquid chromatography coupled to mass spectrometry with HILIC and RPLC separations
journal, September 2009

Impurity Profiling to Match a Nerve Agent to Its Precursor Source for Chemical Forensics Applications
journal, December 2011

XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification
journal, February 2006

Robust Early Pregnancy Prediction of Later Preeclampsia Using Metabolomic Biomarkers
journal, October 2010

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
journal, July 2010

An Enzyme that Regulates Ether Lipid Signaling Pathways in Cancer Annotated by Multidimensional Profiling
journal, October 2006

Algorithms and tools for the preprocessing of LC–MS metabolomics data
journal, August 2011

Screening and analysis of aconitum alkaloids and their metabolites in rat urine after oral administration of aconite roots extract using LC-TOFMS-based metabolomics: Screening and analysis of aconitum alkaloids and their metabolites
journal, March 2011

A comprehensive urinary metabolomic approach for identifying kidney cancer
journal, April 2007

pcaMethods a bioconductor package providing PCA methods for incomplete data
journal, March 2007

Monoacylglycerol Lipase Regulates a Fatty Acid Network that Promotes Cancer Pathogenesis
journal, January 2010

A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar
journal, August 2007

Development of a Robust and Repeatable UPLC−MS Method for the Long-Term Metabolomic Study of Human Serum
journal, January 2009

Urinary Metabonomic Study on Colorectal Cancer
journal, February 2010

Highly sensitive feature detection for high resolution LC/MS
journal, November 2008

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development
journal, January 2009

Metabolic oxidation regulates embryonic stem cell differentiation
journal, May 2010

Expression of hepatitis B virus proteins in transgenic mice alters lipid metabolism and induces oxidative stress in the liver
journal, January 2008

Classifying Degraded Modern Polymeric Museum Artefacts by Their Smell
journal, March 2018

Extraction, chromatographic and mass spectrometric methods for lipid analysis: Review of methods for lipid analysis
journal, February 2016

Coupled Enzymatic Treatment and Mass Spectrometric Analysis for Identification of Glucuronidated Metabolites in Human Samples
journal, May 2019

Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida L.
journal, May 2018

Omics approaches for food authentication
journal, May 2018

Review: Toxicometabolomics: Toxicometabolomics
journal, May 2013

Identification of volatile markers for the detection of adulterants in red ginseng ( Panax ginseng ) juice using headspace stir-bar sorptive extraction coupled with gas chromatography and mass spectrometry
journal, July 2018

Proteomics analysis of tumor microenvironment: Implications of metabolic and oxidative stresses in tumorigenesis: PROTEOMICS ANALYSIS OF TUMOR MICROENVIRONMENT
journal, November 2012

Metabolomics toward personalized medicine
journal, October 2017

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation
journal, November 2017

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
journal, October 2018

Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase: Novel Resorcylic Acid by Stilbene Synthase Mutant
journal, December 2014

Combined maternal and post‐weaning high fat diet inhibits male offspring's prostate cancer tumorigenesis in transgenic adenocarcinoma of mouse prostate model
journal, December 2018

Principal component analysis of normalized full spectrum mass spectrometry data in multiMS-toolbox: An effective tool to identify important factors for classification of different metabolic patterns and bacterial strains
journal, May 2018

Retention time shift analysis and correction in chemical isotope labeling liquid chromatography/mass spectrometry for metabolome analysis
journal, April 2020

Quantitative determination of major platelet activating factors from human plasma
journal, March 2014

Evaluation of changes induced in rice metabolome by Cd and Cu exposure using LC-MS with XCMS and MCR-ALS data analysis strategies
journal, September 2015

Novel analytical methods to study the fate of mycotoxins during thermal food processing
journal, October 2019

Promises and pitfalls of untargeted metabolomics
journal, March 2018

Global metabolomics reveals metabolic dysregulation in ischemic retinopathy
journal, November 2015

Matrix binding of T-2 toxin: structure elucidation of reaction products and indications on the fate of a relevant food-borne toxin during heating
journal, March 2019

Personal genomes, quantitative dynamic omics and personalized medicine
journal, January 2013

The WEIZMASS spectral library for high-confidence metabolite identification
journal, August 2016

Revealing disease-associated pathways by network integration of untargeted metabolomics
journal, August 2016

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
journal, February 2013

The re-emergence of natural products for drug discovery in the genomics era
journal, January 2015

The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation
journal, November 2017

The microbiota regulate neuronal function and fear extinction learning
journal, October 2019

Mass spectrometry searches using MASST
journal, January 2020

Systems-level analysis of isotopic labeling in untargeted metabolomic data by X13CMS
journal, June 2019

Separation of blood microsamples by exploiting sedimentation at the microscale
journal, September 2018

Defining Dysbiosis in Patients with Urolithiasis
journal, April 2019

Starvation-induced collective behavior in C. elegans
journal, May 2015

Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis
journal, August 2015

Metabolomic analysis with GC-MS to reveal potential metabolites and biological pathways involved in Pb & Cd stress response of radish roots
journal, December 2015

Citrate Accumulation-Related Gene Expression and/or Enzyme Activity Analysis Combined With Metabolomics Provide a Novel Insight for an Orange Mutant
journal, July 2016

A global approach to analysis and interpretation of metabolic data for plant natural product discovery
journal, January 2013

Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products
journal, January 2014

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites
journal, January 2017

Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples
journal, January 2019

Metabolic profile analysis of Zhi-zi-chi decoction in feces of normal and chronic unpredictable mild stress-induced depression rats based on UHPLC-ESI-Q-TOF-MS/MS and multiple analytical strategies
journal, January 2019

Onchocerca volvulus -neurotransmitter tyramine is a biomarker for river blindness
journal, February 2013

Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria
journal, June 2017

Beyond monoisotopic accurate mass spectrometry: ancillary techniques for identifying unknown features in non-targeted discovery analysis
journal, November 2018

Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis
journal, September 2015

Low-cost microphysiological systems: Feasibility study of a tape-based barrier-on-chip system for small intestine modeling
posted_content, January 2020

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS
posted_content, January 2020

Drying enhances signal intensity for global GC-MS metabolomics
posted_content, January 2019

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data
posted_content, March 2019

Intestinal peroxisomal fatty acid β-oxidation regulates neural serotonin signaling through a feedback mechanism
posted_content, January 2019

Piezo1 Induces Local Curvature in a Mammalian Membrane and Forms Specific Protein-Lipid Interactions
posted_content, January 2019

Addition of insoluble fiber to isolation media allows for increased metabolite diversity of lab-cultivable microbes derived from zebrafish gut samples
posted_content, January 2019

Behavioural, physiological and molecular changes in alloparental caregivers may be responsible for selection response for female reproductive investment in honey bees
journal, September 2019

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria
journal, May 2016