Tutorial #2: Metabolomics Data Analysis
March 28, 2019. 1:00 p.m. - 4:00 p.m.
Stephen Barnes, Ph.D., Professor Pharmacology & Toxicology at the University of Alabama at Birmingham (UAB),
1:00 – 1:10 p.m. Introduction to the Tutorial Session
This will describe the layout of the tutorial and the options attendees have
Stephen Barnes, Ph.D., UAB/Xiuxia Du, Ph.D. (UNC-Charlotte)
1:10 – 1:50 p.m. Analyzing metabolomics data using MZmine 2
This session will introduce MZmine 2 and explain how to use it for preprocessing LC-MS and GC-MS untargeted metabolomics data.
Note: MZmine 2 should be downloaded from GitHub
1:50 – 2:30 p.m. The principal features of XCMS
XCMS is both an online program and a standalone R program.
Dr. Barnes will demonstrate its capabilities and how to download data on aligned ion features in order to prepare for statistical analysis.
Dr. Du will be available to show those with expertise in R how to use XCMS to process data (instructions will also be in a wiki at Github).
2:30 – 2:40 p.m. 10 minute break
2:40 – 3:20 p.m. Statistical analysis of metabolomics data using Metaboanalyst 4.0
Metaboanalyst is an online, platform-independent statistical and pathway package.
Dr. Barnes will focus on the statistical analysis – files will be available at Github. There is also a R version of this software.
3:20 – 4:00 p.m. Identifying metabolic pathways imbedded in metabolomics data using Mummichog
Mummichog is used to map ion features detected in LC-MS data to metabolites in metabolic pathways. It can be used either as a command line program (Python or Java) or as part of the MZmine 2. Dr. Du will show how to use it as part of MZmine 2 and Dr. Barnes will demonstrate the use of the command line version.