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Grant Details

Grant Number: 5U01CA235493-04 Interpret this number
Primary Investigator: Li, Shuzhao
Organization: Jackson Laboratory
Project Title: Mummichog 3, Aligning Mass Spectrometry Data to Biological Networks
Fiscal Year: 2021


Abstract

Abstract The mummichog software was initially published in 2013, as a computational approach to match patterns in metabolomics data to known biochemical networks, without the requirement of upfront metabolite identification. This approach enables rapid generation of biological hypotheses from untargeted data, and has gained considerable popularity, which also creates urgent needs to upgrade the software itself. This proposal aims to add a rich user interface, and better support of LC-MS, LC- MS/MS, IMS/MS and GC-MS. Furthermore, this work will make a conceptual leap to establish a framework of network alignment as a vehicle to interpret metabolomics data by integrating multiple layers of information. The new development will be integrated into XCMS Online and MetaboAnalyst, and will be made freely available as modular software tools.



Publications

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.
Authors: Pang Z. , Zhou G. , Ewald J. , Chang L. , Hacariz O. , Basu N. , Xia J. .
Source: Nature protocols, 2022 08; 17(8), p. 1735-1761.
EPub date: 2022-06-17.
PMID: 35715522
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Microbial Metabolite 3-Indolepropionic Acid Mediates Immunosuppression.
Authors: Guijas C. , Horton L.E. , Hoang L. , Domingo-Almenara X. , Billings E.M. , Ware B.C. , Sullivan B. , Siuzdak G. .
Source: Metabolites, 2022-07-14; 12(7), .
EPub date: 2022-07-14.
PMID: 35888769
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Metabolite discovery: Biochemistry's scientific driver.
Authors: Giera M. , Yanes O. , Siuzdak G. .
Source: Cell metabolism, 2022-01-04; 34(1), p. 21-34.
PMID: 34986335
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Metabolomics activity screening of T cell-induced colitis reveals anti-inflammatory metabolites.
Authors: Montenegro-Burke J.R. , Kok B.P. , Guijas C. , Domingo-Almenara X. , Moon C. , Galmozzi A. , Kitamura S. , Eckmann L. , Saez E. , Siuzdak G.E. , et al. .
Source: Science signaling, 2021-09-28; 14(702), p. eabf6584.
EPub date: 2021-09-28.
PMID: 34582249
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Single Quadrupole Multiple Fragment Ion Monitoring Quantitative Mass Spectrometry.
Authors: Xue J. , Derks R.J.E. , Webb B. , Billings E.M. , Aisporna A. , Giera M. , Siuzdak G. .
Source: Analytical chemistry, 2021-08-10; 93(31), p. 10879-10889.
EPub date: 2021-07-27.
PMID: 34313111
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MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.
Authors: Pang Z. , Chong J. , Zhou G. , de Lima Morais D.A. , Chang L. , Barrette M. , Gauthier C. , Jacques P.É. , Li S. , Xia J. .
Source: Nucleic acids research, 2021-07-02; 49(W1), p. W388-W396.
PMID: 34019663
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A Practical Guide to Metabolomics Software Development.
Authors: Chang H.Y. , Colby S.M. , Du X. , Gomez J.D. , Helf M.J. , Kechris K. , Kirkpatrick C.R. , Li S. , Patti G.J. , Renslow R.S. , et al. .
Source: Analytical chemistry, 2021-02-02; 93(4), p. 1912-1923.
EPub date: 2021-01-19.
PMID: 33467846
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Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets.
Authors: Pang Z. , Zhou G. , Chong J. , Xia J. .
Source: Metabolites, 2021-01-09; 11(1), .
EPub date: 2021-01-09.
PMID: 33435351
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METLIN MS2 molecular standards database: a broad chemical and biological resource.
Authors: Xue J. , Guijas C. , Benton H.P. , Warth B. , Siuzdak G. .
Source: Nature methods, 2020 10; 17(10), p. 953-954.
PMID: 32839599
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Metabolic adaptation to calorie restriction.
Authors: Guijas C. , Montenegro-Burke J.R. , Cintron-Colon R. , Domingo-Almenara X. , Sanchez-Alavez M. , Aguirre C.A. , Shankar K. , Majumder E.L. , Billings E. , Conti B. , et al. .
Source: Science signaling, 2020-09-08; 13(648), .
EPub date: 2020-09-08.
PMID: 32900879
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Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing.
Authors: Liu Q. , Walker D. , Uppal K. , Liu Z. , Ma C. , Tran V. , Li S. , Jones D.P. , Yu T. .
Source: Scientific reports, 2020-08-17; 10(1), p. 13856.
EPub date: 2020-08-17.
PMID: 32807888
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Cloud-based archived metabolomics data: A resource for in-source fragmentation/annotation, meta-analysis and systems biology.
Authors: Palermo A. , Huan T. , Rinehart D. , Rinschen M.M. , Li S. , O'Donnell V.B. , Fahy E. , Xue J. , Subramaniam S. , Benton H.P. , et al. .
Source: Analytical science advances, 2020 Jun; 1(1), p. 70-80.
EPub date: 2020-06-13.
PMID: 35190800
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MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics.
Authors: Pang Z. , Chong J. , Li S. , Xia J. .
Source: Metabolites, 2020-05-07; 10(5), .
EPub date: 2020-05-07.
PMID: 32392884
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Enhanced in-Source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification.
Authors: Xue J. , Domingo-Almenara X. , Guijas C. , Palermo A. , Rinschen M.M. , Isbell J. , Benton H.P. , Siuzdak G. .
Source: Analytical chemistry, 2020-04-21; 92(8), p. 6051-6059.
EPub date: 2020-04-10.
PMID: 32242660
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Understanding mixed environmental exposures using metabolomics via a hierarchical community network model in a cohort of California women in 1960's.
Authors: Li S. , Cirillo P. , Hu X. , Tran V. , Krigbaum N. , Yu S. , Jones D.P. , Cohn B. .
Source: Reproductive toxicology (Elmsford, N.Y.), 2020 03; 92, p. 57-65.
EPub date: 2019-07-09.
PMID: 31299210
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Network-Based Approaches for Multi-omics Integration.
Authors: Zhou G. , Li S. , Xia J. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 469-487.
PMID: 31953831
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Pathway Analysis for Targeted and Untargeted Metabolomics.
Authors: Karnovsky A. , Li S. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 387-400.
PMID: 31953827
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Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data.
Authors: Chong J. , Xia J. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 337-360.
PMID: 31953825
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The Essential Toolbox of Data Science: Python, R, Git, and Docker.
Authors: Pittard W.S. , Li S. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 265-311.
PMID: 31953823
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A Bioinformatics Primer to Data Science, with Examples for Metabolomics.
Authors: Pittard W.S. , Villaveces C.K. , Li S. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 245-263.
PMID: 31953822
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METLIN: A Tandem Mass Spectral Library of Standards.
Authors: Montenegro-Burke J.R. , Guijas C. , Siuzdak G. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 149-163.
PMID: 31953817
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Metabolomics Data Processing Using XCMS.
Authors: Domingo-Almenara X. , Siuzdak G. .
Source: Methods in molecular biology (Clifton, N.J.), 2020; 2104, p. 11-24.
PMID: 31953810
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Metabolic rewiring of the hypertensive kidney.
Authors: Rinschen M.M. , Palygin O. , Guijas C. , Palermo A. , Palacio-Escat N. , Domingo-Almenara X. , Montenegro-Burke R. , Saez-Rodriguez J. , Staruschenko A. , Siuzdak G. .
Source: Science signaling, 2019-12-10; 12(611), .
EPub date: 2019-12-10.
PMID: 31822592
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Identification of bioactive metabolites using activity metabolomics.
Authors: Rinschen M.M. , Ivanisevic J. , Giera M. , Siuzdak G. .
Source: Nature reviews. Molecular cell biology, 2019 06; 20(6), p. 353-367.
PMID: 30814649
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