Grant Details
| Grant Number: | 7U01CA235493-03 Interpret this number |
| Primary Investigator: | Li, Shuzhao |
| Organization: | Jackson Laboratory |
| Project Title: | Mummichog 3, Aligning Mass Spectrometry Data to Biological Networks |
| Fiscal Year: | 2020 |
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
A fatty acid amide activates myeloid cells and improves neurovascular outcomes in retinal degeneration.
Authors: Wei G. , Chatterjee S. , Yang Q. , Vijayakumar S. , Ogasawara D. , Giles S. , Biscocho K. , Westenskow P. , Wang J. , Fan R. , et al. .
Source: Nature Neuroscience, 2026-06-19 00:00:00.0; , .
EPub date: 2026-06-19 00:00:00.0.
PMID: 42321469
Related Citations
Adaptive Modeling of Tandem Mass Spectrometry Data: Creation of the METLIN 960K MRM Database.
Authors: Aisporna A. , Webb B. , Uritboonthai W. , Hoang L. , Billings E.M. , Hoang C. , Plumb R. , Siuzdak G. .
Source: Analytical Chemistry, 2025-11-11 00:00:00.0; 97(44), p. 24586-24595.
EPub date: 2025-10-28 00:00:00.0.
PMID: 41150651
Related Citations
Constructing a consensus serum metabolome.
Authors: Chi Y. , Mitchell J.M. , Thapa M. , Zheng S. , Frohock Z. , Li Y. , Smirnov A. , Du X. , Li S. .
Source: Biorxiv : The Preprint Server For Biology, 2025-05-11 00:00:00.0; , .
EPub date: 2025-05-11 00:00:00.0.
PMID: 40654862
Related Citations
Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web.
Authors: Mitchell J.M. , Chi Y. , Zheng S. , Thapa M. , Wang E. , Li S. .
Source: Journal Of The American Society For Mass Spectrometry, 2024-12-04 00:00:00.0; 35(12), p. 2824-2835.
EPub date: 2024-09-30 00:00:00.0.
PMID: 39348378
Related Citations
XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis.
Authors: Giera M. , Aisporna A. , Uritboonthai W. , Hoang L. , Derks R.J.E. , Joseph K.M. , Baker E.S. , Siuzdak G. .
Source: Molecular Systems Biology, 2024-09-19 00:00:00.0; , .
EPub date: 2024-09-19 00:00:00.0.
PMID: 39300326
Related Citations
Predicting the Predicted: A Comparison of Machine Learning-Based Collision Cross-Section Prediction Models for Small Molecules.
Authors: de Cripan S.M. , Arora T. , Olomí A. , Canela N. , Siuzdak G. , Domingo-Almenara X. .
Source: Analytical Chemistry, 2024-06-04 00:00:00.0; 96(22), p. 9088-9096.
EPub date: 2024-05-24 00:00:00.0.
PMID: 38783786
Related Citations
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.
Authors: Mitchell J.M. , Chi Y. , Thapa M. , Pang Z. , Xia J. , Li S. .
Source: Plos Computational Biology, 2024 Jun; 20(6), p. e1011912.
EPub date: 2024-06-06 00:00:00.0.
PMID: 38843301
Related Citations
METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification.
Authors: Baker E.S. , Uritboonthai W. , Aisporna A. , Hoang C. , Heyman H.M. , Connell L. , Olivier-Jimenez D. , Giera M. , Siuzdak G. .
Source: Nature Metabolism, 2024-05-27 00:00:00.0; , .
EPub date: 2024-05-27 00:00:00.0.
PMID: 38802544
Related Citations
MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics.
Authors: Pang Z. , Xu L. , Viau C. , Lu Y. , Salavati R. , Basu N. , Xia J. .
Source: Nature Communications, 2024-05-01 00:00:00.0; 15(1), p. 3675.
EPub date: 2024-05-01 00:00:00.0.
PMID: 38693118
Related Citations
Tandem Mass Spectrometry across Platforms.
Authors: Hoang C. , Uritboonthai W. , Hoang L. , Billings E.M. , Aisporna A. , Nia F.A. , Derks R.J.E. , Williamson J.R. , Giera M. , Siuzdak G. .
Source: Analytical Chemistry, 2024-04-09 00:00:00.0; 96(14), p. 5478-5488.
EPub date: 2024-03-26 00:00:00.0.
PMID: 38529642
Related Citations
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation.
Authors: Pang Z. , Lu Y. , Zhou G. , Hui F. , Xu L. , Viau C. , Spigelman A.F. , MacDonald P.E. , Wishart D.S. , Li S. , et al. .
Source: Nucleic Acids Research, 2024-04-08 00:00:00.0; , .
EPub date: 2024-04-08 00:00:00.0.
PMID: 38587201
Related Citations
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline.
Authors: Mitchell J.M. , Chi Y. , Thapa M. , Pang Z. , Xia J. , Li S. .
Source: Biorxiv : The Preprint Server For Biology, 2024-02-14 00:00:00.0; , .
EPub date: 2024-02-14 00:00:00.0.
PMID: 38405981
Related Citations
METLIN-CCS: an ion mobility spectrometry collision cross section database.
Authors: Baker E.S. , Hoang C. , Uritboonthai W. , Heyman H.M. , Pratt B. , MacCoss M. , MacLean B. , Plumb R. , Aisporna A. , Siuzdak G. .
Source: Nature Methods, 2023-11-06 00:00:00.0; , .
EPub date: 2023-11-06 00:00:00.0.
PMID: 37932399
Related Citations
Hydroxyproline metabolism enhances IFN-γ-induced PD-L1 expression and inhibits autophagic flux.
Authors: Spangenberg S.H. , Palermo A. , Gazaniga N.R. , Martínez-Peña F. , Guijas C. , Chin E.N. , Rinschen M.M. , Sander P.N. , Webb B. , Pereira L.E. , et al. .
Source: Cell Chemical Biology, 2023-09-21 00:00:00.0; 30(9), p. 1115-1134.e10.
EPub date: 2023-07-18 00:00:00.0.
PMID: 37467751
Related Citations
Trackable and scalable LC-MS metabolomics data processing using asari.
Authors: Li S. , Siddiqa A. , Thapa M. , Chi Y. , Zheng S. .
Source: Nature Communications, 2023-07-11 00:00:00.0; 14(1), p. 4113.
EPub date: 2023-07-11 00:00:00.0.
PMID: 37433854
Related Citations
A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination.
Authors: Siddiqa A. , Wang Y. , Thapa M. , Martin D.E. , Cadar A.N. , Bartley J.M. , Li S. .
Source: Npj Vaccines, 2023-06-12 00:00:00.0; 8(1), p. 92.
EPub date: 2023-06-12 00:00:00.0.
PMID: 37308481
Related Citations
Generalized Tree Structure to Annotate Untargeted Metabolomics and Stable Isotope Tracing Data.
Authors: Li S. , Zheng S. .
Source: Analytical Chemistry, 2023-04-18 00:00:00.0; 95(15), p. 6212-6217.
EPub date: 2023-04-05 00:00:00.0.
PMID: 37018697
Related Citations
Quantitative multiple fragment monitoring with enhanced in-source fragmentation/annotation mass spectrometry.
Authors: Bernardo-Bermejo S. , Xue J. , Hoang L. , Billings E. , Webb B. , Honders M.W. , Venneker S. , Heijs B. , Castro-Puyana M. , Marina M.L. , et al. .
Source: Nature Protocols, 2023 Apr; 18(4), p. 1296-1315.
EPub date: 2023-02-08 00:00:00.0.
PMID: 36755131
Related Citations
Guiding the choice of informatics software and tools for lipidomics research applications.
Authors: Ni Z. , Wölk M. , Jukes G. , Mendivelso Espinosa K. , Ahrends R. , Aimo L. , Alvarez-Jarreta J. , Andrews S. , Andrews R. , Bridge A. , et al. .
Source: Nature Methods, 2023 Feb; 20(2), p. 193-204.
EPub date: 2022-12-21 00:00:00.0.
PMID: 36543939
Related Citations
Generalized tree structure to annotate untargeted metabolomics and stable isotope tracing data.
Authors: Li S. , Zheng S. .
Source: Biorxiv : The Preprint Server For Biology, 2023-01-04 00:00:00.0; , .
EPub date: 2023-01-04 00:00:00.0.
PMID: 36711587
Related Citations
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data.
Authors: Lu Y. , Pang Z. , Xia J. .
Source: Briefings In Bioinformatics, 2022-12-26 00:00:00.0; , .
EPub date: 2022-12-26 00:00:00.0.
PMID: 36572652
Related Citations
Drug-Initiated Activity Metabolomics Identifies Myristoylglycine as a Potent Endogenous Metabolite for Human Brown Fat Differentiation.
Authors: Guijas C. , To A. , Montenegro-Burke J.R. , Domingo-Almenara X. , Alipio-Gloria Z. , Kok B.P. , Saez E. , Alvarez N.H. , Johnson K.A. , Siuzdak G. .
Source: Metabolites, 2022-08-16 00:00:00.0; 12(8), .
EPub date: 2022-08-16 00:00:00.0.
PMID: 36005620
Related Citations
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 00:00:00.0; 12(7), .
EPub date: 2022-07-14 00:00:00.0.
PMID: 35888769
Related Citations
Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN.
Authors: Aisporna A. , Benton H.P. , Chen A. , Derks R.J.E. , Galano J.M. , Giera M. , Siuzdak G. .
Source: Journal Of The American Society For Mass Spectrometry, 2022-03-02 00:00:00.0; 33(3), p. 530-534.
EPub date: 2022-02-17 00:00:00.0.
PMID: 35174708
Related Citations
Metabolite discovery: Biochemistry's scientific driver.
Authors: Giera M. , Yanes O. , Siuzdak G. .
Source: Cell Metabolism, 2022-01-04 00:00:00.0; 34(1), p. 21-34.
PMID: 34986335
Related Citations
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 00:00:00.0; 14(702), p. eabf6584.
EPub date: 2021-09-28 00:00:00.0.
PMID: 34582249
Related Citations
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 00:00:00.0; 93(31), p. 10879-10889.
EPub date: 2021-07-27 00:00:00.0.
PMID: 34313111
Related Citations
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, 2021-05-21 00:00:00.0; , .
EPub date: 2021-05-21 00:00:00.0.
PMID: 34019663
Related Citations
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 00:00:00.0; 93(4), p. 1912-1923.
EPub date: 2021-01-19 00:00:00.0.
PMID: 33467846
Related Citations
Cognitive analysis of metabolomics data for systems biology.
Authors: Majumder E.L. , Billings E.M. , Benton H.P. , Martin R.L. , Palermo A. , Guijas C. , Rinschen M.M. , Domingo-Almenara X. , Montenegro-Burke J.R. , Tagtow B.A. , et al. .
Source: Nature Protocols, 2021-01-22 00:00:00.0; , .
EPub date: 2021-01-22 00:00:00.0.
PMID: 33483720
Related Citations
Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets.
Authors: Pang Z. , Zhou G. , Chong J. , Xia J. .
Source: Metabolites, 2021-01-09 00:00:00.0; 11(1), .
EPub date: 2021-01-09 00:00:00.0.
PMID: 33435351
Related Citations
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
Related Citations
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 00:00:00.0; 13(648), .
EPub date: 2020-09-08 00:00:00.0.
PMID: 32900879
Related Citations
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 00:00:00.0; 10(1), p. 13856.
EPub date: 2020-08-17 00:00:00.0.
PMID: 32807888
Related Citations
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 00:00:00.0.
PMID: 35190800
Related Citations
MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics.
Authors: Pang Z. , Chong J. , Li S. , Xia J. .
Source: Metabolites, 2020-05-07 00:00:00.0; 10(5), .
EPub date: 2020-05-07 00:00:00.0.
PMID: 32392884
Related Citations
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 00:00:00.0; 92(8), p. 6051-6059.
EPub date: 2020-04-10 00:00:00.0.
PMID: 32242660
Related Citations
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
Related Citations
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
Related Citations
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
Related Citations
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
Related Citations
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
Related Citations
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
Related Citations
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
Related Citations
The METLIN small molecule dataset for machine learning-based retention time prediction.
Authors: Domingo-Almenara X. , Guijas C. , Billings E. , Montenegro-Burke J.R. , Uritboonthai W. , Aisporna A.E. , Chen E. , Benton H.P. , Siuzdak G. .
Source: Nature Communications, 2019-12-20 00:00:00.0; 10(1), p. 5811.
EPub date: 2019-12-20 00:00:00.0.
PMID: 31862874
Related Citations
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 00:00:00.0; 12(611), .
EPub date: 2019-12-10 00:00:00.0.
PMID: 31822592
Related Citations
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.), 2019-07-09 00:00:00.0; , .
EPub date: 2019-07-09 00:00:00.0.
PMID: 31299210
Related Citations
Identification of bioactive metabolites using activity metabolomics.
Authors: Rinschen M.M. , Ivanisevic J. , Giera M. , Siuzdak G. .
Source: Nature Reviews. Molecular Cell Biology, 2019 Jun; 20(6), p. 353-367.
PMID: 30814649
Related Citations