Course Schedule
Schedule for May 26 - May 27, 2016
Workshop Q/A Forum
Post your workshop questions here!
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
Pre-workshop Readings
Before coming to the workshop, read these.
XCMS Online: a web-based platform to process untargeted metabolic data
Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics
HMDB 3.0 - The Human Metabolome Database in 2013
Introduction to Cheminformatics
Class Picture
YouTube Playlist for Recorded Lectures
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Metabolomics
David Wishart
Module 2: Metabolite Identification and Annotation
David Wishart and Jeff Xia
Break-out Groups:
Begin with your assigned data set and then move through to the next data set when done.
Student #01-10 - Begin with NMR and Bayesil.
Sub-groups for NMR
| Students | Data Set |
|---|---|
| 1-2 | #1 |
| 3-4 | #2 |
| 5-6 | #3 |
| 7-8 | #4 |
| 9-10 | #5 |
Student #11-20 - Begin with GC-MS and GCMS.
Student #21-34 - Begin with LC-MS and XCMS Online. note: seems to be working now
Data Set and Results Files:
NMR:
GC-MS:
LC-MS:
Small test datasets:
Description: a subset of 12 samples from the study Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling.
Group WT: wild type; Group KO: knock out. Platform: HPLC Single Quad.
Large test datasets (warning: may take ~2 hours to upload this dataset to the XCMS Online server!):
Description: a subset of 38 samples from the study Pregnancy-Induced Metabolic Phenotype Variations in Maternal Plasma.
Group A: 13-16 weeks; Group B: 9-12 weeks. Platform: HPLC Orbitrap
Links:
- MetaboMiner
- rNMR
- BMRB Peaks Server
- BATMAN
- Bayesil
- Golm Database
- NIST/AMDIS
- CFM-ID
- Metlin
- MetFusion
- Adduct Table
- MZedDB
- MWTWIN
- HighChem
- 7GR Software
- MyCompoundID
Module 2 Data Output
Place your data file in this google folder.
Module 3: Databases for Chemical, Spectral, and Biological Data
David Wishart
Links:
- HMDB
- DrugBank
- METLIN
- PubChem
- ChEBI
- ChemSpider
- SDBS
- BioMagResBank
- MMCD
- MassBank
- BMRB
- NMRShiftDB
- SMPDB
- KEGG
- Reactome
- BioCyc
Day 2
Module 4: Backgrounder in Statistical Methods
Jeff Xia
Module 5: MetaboAnalyst
David Wishart and Jeff Xia
Extras:
Data Input:
Critical: before uploading your data, perform a sanity check:
- It is a data table separated by comma (.csv) or tab (.txt);
- Three types of labels: feature names, sample names and group labels (must directly follow sample names);
- All measurements should be numerical values (empty for missing values);
-
For details and screenshot instructions, click here
- CBW_NMR_result.csv (Bayesil output - need to remove annotations lines starting with #, keep one type of ID - name/HMDB ID)
- CBW_GCMS_examples_cleaned_2015.csv (Auto-GCMS output - need to remove <LOD and NA values )
- FAAH_cleaned_metaboanalyst.csv (peak intensity table from XCMSonline - small LC-MS data)
- XCMS_cleaned_metaboanalyst.csv (peak intensity table from XCMSonline - big LC-MS data)
Module 6: Future of Metabolomics
David Wishart