Informatics and Statistics for Metabolomics 2016

Workshop pages for students

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

Class Picture

Link to download picture

YouTube Playlist for Recorded Lectures

Recorded Lectures’ Playlist

Day 1


Ann Meyer

Module 1: Introduction to Metabolomics

David Wishart


Recorded Lecture

Module 2: Metabolite Identification and Annotation

David Wishart and Jeff Xia


Recorded Lecture

Lab practical

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:


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

Module 2 Data Output

Place your data file in this google folder.

Module 3: Databases for Chemical, Spectral, and Biological Data

David Wishart


Recorded Lecture

Day 2

Module 4: Backgrounder in Statistical Methods

Jeff Xia


Recorded Lecture

Module 5: MetaboAnalyst

David Wishart and Jeff Xia


Recorded Lecture

Lab practical


MetaboAnalyst Tutorial 1

MetaboAnalyst Tutorial 2

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


Recorded Lecture

Link to survey

View on GitHub