Laptop Setup Instructions
Instructions for setting up your laptop can be found here: Laptop Setup Instructions
Pre-Workshop Readings
Current Progress in Computational Metabolomics
Computational Strategies for Metabolite Identification
HMDB: The Human Metabolome Database in 2013 PMC3531200
Metabolomic Data Processing, Analysis, and Interpretation Using MetaboAnalyst
MetaboAnalyst 3.0-making metabolomics more meaningful
Day 1
Welcome
*Faculty: Michelle Brazas*Module 1: Introduction to Metabolomics
*Faculty: David Wishart*Lecture:
Metabolomics2015_Module1.pdf
Metabolomics2015_Module1.ppt
Metabolomics2015_Module1.mp4
Module 2: Software for Metabolite ID and Quantification
*Faculty: David Wishart*Lecture:
Metabolomics2015_Module2.pdf
Metabolomics2015_Module2.ppt
Metabolomics2015_Module2.mp4
Lab Practical:
Faculty: Jeff Xia
Metabolomics2015_Module2_lab.pdf
Break-out Groups:
Begin in your assigned data set and then move through to the next data set when done
- Student #01-10 - Begin with NMR and CBW-Bayesil
Sub-groups for NMR - Students 1-2: Use Data Set#1
Sub-groups for NMR - Students 3-4: Use Data Set#2
Sub-groups for NMR - Students 5-6: Use Data Set#3
Sub-groups for NMR - Students 7-8: Use Data Set#4
Sub-groups for NMR - Students 9-10: Use Data Set#5
- Student #11-20 - Begin with GC-MS and GCMS
- Student #21-34 - Begin with LC-MS and XCMS Online
Data Set and Results Files:
NMR
GC-MS
LC-MS:
Small test datasets:
Description: a subset of 12 samples from a 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 a 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 3: Databases for Chemical, Spectral and bIological Data
Faculty: David Wishart
Lecture:
Metabolomics2015_Module3.pdf
Metabolomics2015_Module3.ppt
Metabolomics2015_Module3.mp4
Links:
* HMDB
* DrugBank
* METLIN
* PubChem
* ChEBI
* ChemSpider
* SDBS
* BioMagResBank
* MMCD
* MassBank
* BMRB
* NMRShiftDB
* SMPDB
* KEGG
* Reactome
* BioCyc
Day 2
Module 4: Backgrounder in Statistics
Faculty: David Wishart
Lecture:
Metabolomics2015_Module4.pdf
Metabolomics2015_Module4.ppt
Metabolomics2015_Module4.mp4
Module 5: MetaboAnalyst
Faculty: David Wishart
Lecture:
Metabolomics2015_Module5.pdf
Metabolomics2015_Module5.ppt
Metabolomics2015_Module5.mp4
Lab: MetaboAnalyst Data Analysis using MetaboAnalyst 3.0
Faculty: Jeff Xia
Metabolomics2015_Module5_Lab.pdf
MetaboAnalyst Websites:
We have set up multiple mirror sites of the server. Please use your student # (on the front of your name badge) to access the mirror for your student #:
* Student # 01-08 - www.metaboanalyst.ca
* Student # 08-16 - mirror.metaboanalyst.ca
* Student # 17-24 - mirror1.metaboanalyst.ca
* Student # 25-32 - mirror2.metaboanalyst.ca
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: 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
Faculty: David Wishart
Lecture: