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
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; 12(7), .
EPub date: 2022-07-14.
PMID: 35888769
Related Citations
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
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; 14(702), p. eabf6584.
EPub date: 2021-09-28.
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; 93(31), p. 10879-10889.
EPub date: 2021-07-27.
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, 2021-07-02; 49(W1), p. W388-W396.
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; 93(4), p. 1912-1923.
EPub date: 2021-01-19.
PMID: 33467846
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; 11(1), .
EPub date: 2021-01-09.
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; 13(648), .
EPub date: 2020-09-08.
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; 10(1), p. 13856.
EPub date: 2020-08-17.
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.
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; 10(5), .
EPub date: 2020-05-07.
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; 92(8), p. 6051-6059.
EPub date: 2020-04-10.
PMID: 32242660
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.), 2020 03; 92, p. 57-65.
EPub date: 2019-07-09.
PMID: 31299210
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
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
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
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
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
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
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
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
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 06; 20(6), p. 353-367.
PMID: 30814649
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