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Informatics and Statistics for Metabolomics 2015

Workshop pages for students


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

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:

Metabolomics2015_Module6.pdf
Metabolomics2015_Module6.ppt

View on GitHub