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Title: Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism

Abstract

Although the objective of any ‘omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used, respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. In this work, the combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a singlemore » biological extract, using 80% organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [3];  [1]
+ Show Author Affiliations
  1. The Scripps Research Inst., La Jolla, CA (United States)
  2. La Jolla Laboratories, San Diego, CA (United States). Pfizer Worldwide Research and Development
  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), Biological and Environmental Research (BER); California Institute of Regenerative Medicine; National Institutes of Health (NIH); National Institute on Aging (NIA)
OSTI Identifier:
1788443
Grant/Contract Number:  
AC02-05CH11231; FG02-07ER64325
Resource Type:
Accepted Manuscript
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 85; 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; Metabolism; Chromatography; Ionization; Cells; Computational chemistry

Citation Formats

Ivanisevic, Julijana, Zhu, Zheng-Jiang, Plate, Lars, Tautenhahn, Ralf, Chen, Stephen, O’Brien, Peter J., Johnson, Caroline H., Marletta, Michael A., Patti, Gary J., and Siuzdak, Gary. Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism. United States: N. p., 2013. Web. doi:10.1021/ac401140h.
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Ivanisevic, Julijana, Zhu, Zheng-Jiang, Plate, Lars, Tautenhahn, Ralf, Chen, Stephen, O’Brien, Peter J., Johnson, Caroline H., Marletta, Michael A., Patti, Gary J., & Siuzdak, Gary. Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism. United States. https://doi.org/10.1021/ac401140h
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Ivanisevic, Julijana, Zhu, Zheng-Jiang, Plate, Lars, Tautenhahn, Ralf, Chen, Stephen, O’Brien, Peter J., Johnson, Caroline H., Marletta, Michael A., Patti, Gary J., and Siuzdak, Gary. Wed . "Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism". United States. https://doi.org/10.1021/ac401140h. https://www.osti.gov/servlets/purl/1788443.
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@article{osti_1788443,
title = {Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism},
author = {Ivanisevic, Julijana and Zhu, Zheng-Jiang and Plate, Lars and Tautenhahn, Ralf and Chen, Stephen and O’Brien, Peter J. and Johnson, Caroline H. and Marletta, Michael A. and Patti, Gary J. and Siuzdak, Gary},
abstractNote = {Although the objective of any ‘omic science is broad measurement of its constituents, such coverage has been challenging in metabolomics because the metabolome is comprised of a chemically diverse set of small molecules with variable physical properties. While extensive studies have been performed to identify metabolite isolation and separation methods, these strategies introduce bias toward lipophilic or water-soluble metabolites depending on whether reversed-phase (RP) or hydrophilic interaction liquid chromatography (HILIC) is used, respectively. Here we extend our consideration of metabolome isolation and separation procedures to integrate RPLC/MS and HILIC/MS profiling. An aminopropyl-based HILIC/MS method was optimized on the basis of mobile-phase additives and pH, followed by evaluation of reproducibility. When applied to the untargeted study of perturbed bacterial metabolomes, the HILIC method enabled the accurate assessment of key, dysregulated metabolites in central carbon pathways (e.g., amino acids, organic acids, phosphorylated sugars, energy currency metabolites), which could not be retained by RPLC. To demonstrate the value of the integrative approach, bacterial cells, human plasma, and cancer cells were analyzed by combined RPLC/HILIC separation coupled to ESI positive/negative MS detection. In this work, the combined approach resulted in the observation of metabolites associated with lipid and central carbon metabolism from a single biological extract, using 80% organic solvent (ACN:MeOH:H2O 2:2:1). It enabled the detection of more than 30,000 features from each sample type, with the highest number of uniquely detected features by RPLC in ESI positive mode and by HILIC in ESI negative mode. Therefore, we conclude that when time and sample are limited, the maximum amount of biological information related to lipid and central carbon metabolism can be acquired by combining RPLC ESI positive and HILIC ESI negative mode analysis.},
doi = {10.1021/ac401140h},
journal = {Analytical Chemistry},
number = 14,
volume = 85,
place = {United States},
year = {Wed Jun 19 00:00:00 EDT 2013},
month = {Wed Jun 19 00:00:00 EDT 2013}
}
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    The Blood Exposome and Its Role in Discovering Causes of Disease
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    • Rappaport, Stephen M.; Barupal, Dinesh K.; Wishart, David
    • Environmental Health Perspectives, Vol. 122, Issue 8
    • DOI: 10.1289/ehp.1308015

    Biomonitoring in the Era of the Exposome
    journal, April 2017

    • Dennis, Kristine K.; Marder, Elizabeth; Balshaw, David M.
    • Environmental Health Perspectives, Vol. 125, Issue 4
    • DOI: 10.1289/ehp474

    A Fatal Combination: A Thymidylate Synthase Inhibitor with DNA Damaging Activity
    journal, February 2015

    Untargeted mass spectrometry discloses plasma solute levels poorly controlled by hemodialysis
    journal, November 2017

    Cancer proteome and metabolite changes linked to SHMT2
    journal, September 2020

    Metabolomic strategies for the identification of new enzyme functions and metabolic pathways
    journal, May 2014

    • Prosser, Gareth A.; Larrouy‐Maumus, Gerald; Carvalho, Luiz Pedro S.
    • EMBO reports, Vol. 15, Issue 6
    • DOI: 10.15252/embr.201338283

    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

    MetabNet: An R Package for Metabolic Association Analysis of High-Resolution Metabolomics Data
    journal, June 2015

    • Uppal, Karan; Soltow, Quinlyn A.; Promislow, Daniel E. L.
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00087

    Cigarette Smoke Reduces Fatty Acid Catabolism, Leading to Apoptosis in Lung Endothelial Cells: Implication for Pathogenesis of COPD
    journal, August 2019

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

    Application of the amniotic fluid metabolome to the study of fetal malformations, using Down syndrome as a specific model
    journal, May 2017

    • Huang, Jun; Mo, Jinhua; Zhao, Guili
    • Molecular Medicine Reports, Vol. 16, Issue 5
    • DOI: 10.3892/mmr.2017.7507
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