Advanced special topics course in metabolomics 2022
(GBSC 724)

Course Description

Course will be held on Mondays, Wednesdays and Fridays 9-10:30 am in the SHELBY 1015

Tentative Schedule

Date Lecturer Topic
Jan 10, Mon S. Barnes Transition from metabolism to metabolomics and targeted/untargeted approaches [PDF File]
Jan 12, Wed S. Barnes The extraordinary chemistry of the metabolome [PDF File]
Jan 14, Fri H Tiwari Designing a complex metabolomics experiment [PDF File]
Jan 17, Mon No class Martin Luther King Holiday
Jan 19, Wed J. Prasain Extracting the metabolome (fluids, cells and tissues) [PDF File]
Jan 21, Fri W. Placzek The platform - fundamentals in NMR and metabolomics [PDF File]
Jan 24, Mon S. Barnes The platform – fundamentals in GC- and LC-mass spectrometry [PDF File]
Jan 26, Wed D. Sharer Targeted metabolomics for congenital disease in children [PDF File]
Jan 28, Fri J. Prasain MSMS of small molecules - interpretation [PDF File] [Exercise]
Jan 31, Mon J. Prasain
S. Barnes
SWATH-MS, Ion Mobility and LC-MS for lipidomics
[PDF File 1] [PDF File 2] [PDF File 3]
Feb 2, Wed J. Kabarowski Lipid imaging-mass spectrometry [PDF File]
Feb 4, Fri J. Prasain Lipid maps database [PDF File]
Feb 7, Mon J. Prasain Validating metabolites and Novel prostanoid molecules [PDF File]
Feb 9, Wed W. Placzek Processing NMR data [PDF File]
Feb 11, Fri   Students’ presentations
Feb 14, Mon S. Barnes MS-DIAL 4.80 – a comprehensive metabolomics tool – bring PC [PDF File]
Feb 16, Wed P. Dorrestein
M. Wang***
Deep MSMS analysis with GNPS
Feb 18, Fri S. Barnes Statistical analysis of MS-DIAL data with MetaboAnalyst 5.0
Feb 21 Mon S. Barnes MZmine 2.53 hands-on class exercise [PDF File]
Feb 23, Wed S. Barnes Peak detection and alignment - MZmine
Feb 25, Fri   The TMAO story and follow up – Students’ presentations [Reference]
Feb 28, Mon S. Barnes Bile acid metabolism
Mar 2, Wed R. Quinn**** Exploration of bile acid conjugation with GNPS
Mar 4, Fri S. Barnes Pathway databases and metabolomics workbench
Mar 6, Mon C. Beecher* Isotope Ratio Outlier Analysis (IROA) [Video]
Mar 9, Wed C. Beecher* Building a metabolite standards database
Mar 11, Fri S. Barnes Uploading GC-MS and LC-MS data to XCMSonline [PDF File]
Mar 14, Mon S. Barnes Metaboanalyst analysis of XCMS data files
Mar 16, Wed S. Barnes Peaks-to-pathways - Mummichog analysis of data
Mar 18, Fri S. Barnes Isotopes and pathway dynamics [PDF File]
Mar 21, Mon S. Barnes In situ lipidomics in the surgical suite [PDF File]
Mar 23, Wed X. Hu** Integration of -omics data
Mar 25, Fri   Student presentations
Mar 28, Mon Laura Reed (UA) Integrating the metabolome with the genome and transcriptome in the context of environmental exposure in the fruit fly [PDF File]
Mar 29, Tue Rafael Montenegro-Burke (U Toronto) The dark metabolome – video (sponsored by Thermo)
Mar 30, Wed S. Barnes Class discussion about the dark metabolome
Apr 1, Fri T. Marquez-Lago Machine learning and artificial intelligence and its application to metabolomics – and student presentations
Apr 4, Mon S. Barnes Comparing the metabolome between plasma and serum from the same patients – a Metaboanalyst analysis
Apr 6, Wed Jianhua Zhang Integrating metabolomics with mitochondrial function and student paper presentations
Apr 8, Fri S. Barnes Using xMWAS [PDF File]
Apr 11, Mon   FINAL exam due

*At this time, the standalone software we will use, .abc generator, MS-DIAL and MSConvert, work only on a PC. Some software, e.g., Metaboanalyst 5.0, will be used with browsers and are platform-independent

**Xin Hu is from Emory University in Atlanta

***Pieter Dorrestein and Mingxun Wang are from UCSD

****Robert Quinn is from Michigan State University