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

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 canmore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [1];  [1];  [1];  [2];  [2];  [3];  [1]
+ Show Author Affiliations
  1. The Scripps Research Inst., La Jolla, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Washington Univ., St. Louis, MO (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); California Institute of Regenerative Medicine; National Institutes of Health (NIH)
OSTI Identifier:
1788440
Grant/Contract Number:  
AC02-05CH11231; R01 CA170737; R24 EY017540; P30 MH062261; RC1 HL101034; P01 DA026146; R01 ES022181; L30 AG0038036; FG02-07ER64325
Resource Type:
Accepted Manuscript
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 86; Journal Issue: 14; 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; Stress; Bubbles; Metabolomics; Metabolism; Mathematical methods

Citation Formats

Gowda, Harsha, Ivanisevic, Julijana, Johnson, Caroline H., Kurczy, Michael E., Benton, H. Paul, Rinehart, Duane, Nguyen, Thomas, Ray, Jayashree, Kuehl, Jennifer, Arevalo, Bernardo, Westenskow, Peter D., Wang, Junhua, Arkin, Adam P., Deutschbauer, Adam M., Patti, Gary J., and Siuzdak, Gary. Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses. United States: N. p., 2014. Web. doi:10.1021/ac500734c.
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Gowda, Harsha, Ivanisevic, Julijana, Johnson, Caroline H., Kurczy, Michael E., Benton, H. Paul, Rinehart, Duane, Nguyen, Thomas, Ray, Jayashree, Kuehl, Jennifer, Arevalo, Bernardo, Westenskow, Peter D., Wang, Junhua, Arkin, Adam P., Deutschbauer, Adam M., Patti, Gary J., & Siuzdak, Gary. Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses. United States. https://doi.org/10.1021/ac500734c
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Gowda, Harsha, Ivanisevic, Julijana, Johnson, Caroline H., Kurczy, Michael E., Benton, H. Paul, Rinehart, Duane, Nguyen, Thomas, Ray, Jayashree, Kuehl, Jennifer, Arevalo, Bernardo, Westenskow, Peter D., Wang, Junhua, Arkin, Adam P., Deutschbauer, Adam M., Patti, Gary J., and Siuzdak, Gary. Mon . "Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses". United States. https://doi.org/10.1021/ac500734c. https://www.osti.gov/servlets/purl/1788440.
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@article{osti_1788440,
title = {Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses},
author = {Gowda, Harsha and Ivanisevic, Julijana and Johnson, Caroline H. and Kurczy, Michael E. and Benton, H. Paul and Rinehart, Duane and Nguyen, Thomas and Ray, Jayashree and Kuehl, Jennifer and Arevalo, Bernardo and Westenskow, Peter D. and Wang, Junhua and Arkin, Adam P. and Deutschbauer, Adam M. and Patti, Gary J. and Siuzdak, Gary},
abstractNote = {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.},
doi = {10.1021/ac500734c},
journal = {Analytical Chemistry},
number = 14,
volume = 86,
place = {United States},
year = {Mon Jun 16 00:00:00 EDT 2014},
month = {Mon Jun 16 00:00:00 EDT 2014}
}
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    From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data
    journal, December 2019

    Antioxidant Activity of the Lignins Derived from Fluidized-Bed Fast Pyrolysis
    journal, March 2017

    Untargeted Metabolite Profiling for Screening Bioactive Compounds in Digestate of Manure under Anaerobic Digestion
    journal, November 2019

    • Lu, Jiaxin; Muhmood, Atif; Czekała, Wojciech
    • Water, Vol. 11, Issue 11
    • DOI: 10.3390/w11112420

    Non-specific activities of the major herbicide-resistance gene BAR
    text, January 2017

    • Christ, Bastien; Hochstrasser, Ramon; Guyer, Luzia
    • Nature Publishing Group
    • DOI: 10.5167/uzh-148877

    Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function
    journal, April 2018

    • Clark, Chase M.; Costa, Maria S.; Sanchez, Laura M.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 19
    • DOI: 10.1073/pnas.1801247115

    WebSpecmine: a website for metabolomics data analysis and mining.
    conference, November 2018

    • Cardoso, Sara; Afonso, Telma; Maraschin, Marcelo
    • Proceedings of 3rd International Electronic Conference on Metabolomics
    • DOI: 10.3390/iecm-3-05842

    Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery
    journal, August 2017

    • Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya
    • Journal of Inherited Metabolic Disease, Vol. 41, Issue 3
    • DOI: 10.1007/s10545-017-0080-0

    Brain Region Mapping Using Global Metabolomics
    journal, November 2014

    Blood transcriptomics and metabolomics for personalized medicine
    journal, January 2016

    • Li, Shuzhao; Todor, Andrei; Luo, Ruiyan
    • Computational and Structural Biotechnology Journal, Vol. 14
    • DOI: 10.1016/j.csbj.2015.10.005

    LC-HRMS data as a result of untargeted metabolomic profiling of human cerebrospinal fluid
    journal, December 2018

    Evaluation of freely available software tools for untargeted quantification of 13C isotopic enrichment in cellular metabolome from HR-LC/MS data
    journal, June 2020

    • Dange, Manohar C.; Mishra, Vivek; Mukherjee, Bratati
    • Metabolic Engineering Communications, Vol. 10
    • DOI: 10.1016/j.mec.2019.e00120

    Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling
    journal, December 2014

    • Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.
    • Analytical Chemistry, Vol. 87, Issue 2
    • DOI: 10.1021/ac5025649

    Bioinformatics: The Next Frontier of Metabolomics
    journal, November 2014

    • Johnson, Caroline H.; Ivanisevic, Julijana; Benton, H. Paul
    • Analytical Chemistry, Vol. 87, Issue 1
    • DOI: 10.1021/ac5040693

    Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses
    journal, September 2016

    • Montenegro-Burke, J. Rafael; Phommavongsay, Thiery; Aisporna, Aries E.
    • Analytical Chemistry, Vol. 88, Issue 19
    • DOI: 10.1021/acs.analchem.6b02676

    A hybrid polyketide–nonribosomal peptide in nematodes that promotes larval survival
    journal, August 2016

    • Shou, Qingyao; Feng, Likui; Long, Yaoling
    • Nature Chemical Biology, Vol. 12, Issue 10
    • DOI: 10.1038/nchembio.2144

    A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome
    journal, September 2019

    Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer’s Disease
    journal, June 2018

    Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins
    journal, July 2018

    Concurrent profiling of polar metabolites and lipids in human plasma using HILIC-FTMS
    journal, November 2016

    • Cai, Xiaoming; Li, Ruibin
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep36490

    Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis
    journal, December 2016

    • Li, Bo; Tang, Jing; Yang, Qingxia
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep38881

    The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources
    journal, August 2018

    • Mathé, Ewy; Hays, John; Stover, Daniel
    • Yearbook of Medical Informatics, Vol. 27, Issue 01
    • DOI: 10.1055/s-0038-1667085

    N -acyl taurines are endogenous lipid messengers that improve glucose homeostasis
    journal, November 2019

    • Grevengoed, Trisha J.; Trammell, Samuel A. J.; McKinney, Michele K.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 49
    • DOI: 10.1073/pnas.1916288116

    Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function
    posted_content, January 2018

    • Clark, Chase M.; Costa, Maria S.; Sanchez, Laura M.
    • bioRxiv
    • DOI: 10.1101/215350

    Elucidation of complexity and prediction of interactions in microbial communities
    journal, August 2017

    • Zuñiga, Cristal; Zaramela, Livia; Zengler, Karsten
    • Microbial Biotechnology, Vol. 10, Issue 6
    • DOI: 10.1111/1751-7915.12855

    A metabolome-based core hybridisation strategy for the prediction of rice grain weight across environments
    journal, November 2018

    • Dan, Zhiwu; Chen, Yunping; Xu, Yanghong
    • Plant Biotechnology Journal, Vol. 17, Issue 5
    • DOI: 10.1111/pbi.13024

    MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics
    journal, October 2017

    Untargeted metabolomic on urine samples after α-lipoic acid and/or eicosapentaenoic acid supplementation in healthy overweight/obese women
    journal, May 2018

    • Romo-Hualde, Ana; Huerta, Ana E.; González-Navarro, Carlos J.
    • Lipids in Health and Disease, Vol. 17, Issue 1
    • DOI: 10.1186/s12944-018-0750-4

    Amelioration of biomass and lipid in marine alga by an endophytic fungus Piriformospora indica
    journal, July 2019

    • Bhatnagar, Vipul Swarup; Bandyopadhyay, Prasun; Rajacharya, Girish H.
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1516-6

    Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipids
    journal, October 2017

    • Johnson, Caroline H.; Santidrian, Antonio F.; LeBoeuf, Sarah E.
    • Cancer & Metabolism, Vol. 5, Issue 1
    • DOI: 10.1186/s40170-017-0171-2

    Enabling Metabolomics Based Biomarker Discovery Studies Using Molecular Phenotyping of Exosome-Like Vesicles
    journal, March 2016

    Metabolic drift in the aging brain
    journal, May 2016

    • Ivanisevic, Julijana; Stauch, Kelly L.; Petrascheck, Michael
    • Aging, Vol. 8, Issue 5
    • DOI: 10.18632/aging.100961

    Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants
    journal, October 2015

    • Hill, Camilla Beate; Czauderna, Tobias; Klapperstück, Matthias
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00167

    Plasma Lipid Profiling Identifies Biomarkers of Cerebral Microvascular Disease
    journal, August 2019

    Stimulatory Effects of Acibenzolar-S-Methyl on Chlorogenic Acids Biosynthesis in Centella asiatica Cells
    journal, September 2016

    • Ncube, Efficient N.; Steenkamp, Paul A.; Madala, Ntakadzeni E.
    • Frontiers in Plant Science, Vol. 7
    • DOI: 10.3389/fpls.2016.01469

    Profiling of Altered Metabolomic States in Nicotiana tabacum Cells Induced by Priming Agents
    journal, October 2016

    • Mhlongo, Msizi I.; Steenkamp, Paul A.; Piater, Lizelle A.
    • Frontiers in Plant Science, Vol. 7
    • DOI: 10.3389/fpls.2016.01527

    Cannabinoid Profiling of Hemp Seed Oil by Liquid Chromatography Coupled to High-Resolution Mass Spectrometry
    journal, February 2019

    • Citti, Cinzia; Linciano, Pasquale; Panseri, Sara
    • Frontiers in Plant Science, Vol. 10
    • DOI: 10.3389/fpls.2019.00120

    Cytokinin Detection during the Dictyostelium discoideum Life Cycle: Profiles Are Dynamic and Affect Cell Growth and Spore Germination
    journal, November 2019

    • Aoki, Megan; Kisiala, Anna; Li, Shaojun
    • Biomolecules, Vol. 9, Issue 11
    • DOI: 10.3390/biom9110702

    Targeted and Untargeted Metabolomics as an Enhanced Tool for the Detection of Pomegranate Juice Adulteration
    journal, June 2019

    • Dasenaki, Marilena E.; Drakopoulou, Sofia K.; Aalizadeh, Reza
    • Foods, Vol. 8, Issue 6
    • DOI: 10.3390/foods8060212

    Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles
    journal, June 2015

    • Hauschild, Anne-Christin; Frisch, Tobias; Baumbach, Jörg
    • Metabolites, Vol. 5, Issue 2
    • DOI: 10.3390/metabo5020344

    RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites
    journal, February 2018

    Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells
    journal, January 2019

    • Warth, Benedikt; Palermo, Amelia; Rattray, Nicholas J. W.
    • Metabolites, Vol. 9, Issue 1
    • DOI: 10.3390/metabo9010007

    Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite
    journal, November 2019

    • Bearden, Daniel W.; Sheen, David A.; Simón-Manso, Yamil
    • Metabolites, Vol. 9, Issue 11
    • DOI: 10.3390/metabo9110270

    From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data
    journal, December 2019

    Antioxidant Activity of the Lignins Derived from Fluidized-Bed Fast Pyrolysis
    journal, March 2017

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