Advanced special topics course in metabolomics 2022
(GBSC 724)
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