Informatics and Statistics for Metabolomics 2018

Welcome

Informatics and Statistics for Metabolomics.

The course schedule can be found here.

Pre-readings, pre-work, and laptop setup instructions can be found here.

We are using Google Classroom for discussion. Join the Class at https://classroom.google.com, select the “+” symbol in the upper right corner, click on “Join Class” and enter the class code provided to you.

The full course notes are available as a single PDF.

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Class photo

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Day 1

Welcome

Ann Meyer

Module 1: Introduction to Metabolomics

David Wishart

Lecture

Recording

Module 2: Metabolite Identification and Annotation

David Wishart

Lecture

Recording

Lab practical

Instructions for lab

1. NMR and Bayesil.

2. GC-MS and GCMS.

3. LC-MS and XCMS in R. If R doesn’t work, try XCMS online.

Data Set and Results Files:

NMR:

• CBW_NMR_Data.zip
• CBW_NMR_result.zip

• NMR simple example file

GC-Autofit:

Download this file

LC-MS:

Metadata

Raw datasets (raw.zip files)

CKD raw
Control raw

Converted datasets (mzxml.zip files)

CDK mzxml
Control mzxml

XCMS using R (results files)

Diffreport
Peak Table

XCMS online (results files)

Cleaned Diffreport
Normalized Results
Unnormalized Results

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

David Wishart

Lecture

Recording

Links:

• HMDB
• DrugBank
• METLIN
• PubChem
• ChEBI
• ChemSpider
• SDBS
• BioMagResBank
• MMCD
• MassBank
• BMRB
• NMRShiftDB
• SMPDB
• KEGG
• Reactome
• BioCyc

Day 2

Module 4: Backgrounder in Statistics

Jeff Xia

Lecture

Recording

Module 5: MetaboAnalyst

Jeff Xia

Lecture

Recording

Lab practical

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

• You may have downloaded the NMR results .zip folder yesterday. You will need the .csv file from the .zip folder. NMR results.zip (Bayesil output - need to remove annotations lines starting with #, keep one type of ID - name/HMDB ID)
• Cleaned GCMS results (Auto-GCMS output that has been cleaned for you)
• Normalized LCMS csv

• Unnormalized LCMS csv

  Module 6: Future of Metabolomics

  David Wishart

  Lecture

  Recording

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