Introduction to Untargeted Metabolomics Data Analaysis in R using struct and structToolbox packages

Gavin Rhys Lloyd, Ossama Edbali and Ralf Weber

2026-05-19

Preface

This material introduces the use of struct and structToolbox packages to analyse untargeted LCMS metabolomics data sets. It is primarily intended as required pre-course training material for attendees of the Birmingham Metabolomics Training Centre (BMTC), but can also be used as a standalone lesson. The lesson includes:

• Instructions on how to get started
• An introduction to the R-package struct and its templates
• Downloading data from Metabolomics Workbench using R-package metabolomicsWorkBenchR
• Building simple data processing workflows using the pre-built templates in structToolbox

If you have any questions, contact us by email.

Prerequisites

For this course we assume that you have basic programming skills in R. It is not the purpose of this course to teach you R programming. If you are new to R, or need a refresher, we recommend any of the following data carpentry courses:

• Data Analysis and Visualisation in R for Ecologists
• Introduction to R
• R for Reprodicible Scientific Analysis
• Programming with R

Using this document

The material for this course has been divided into modules. You can access the modules using the navigation menu on the left hand side. To view the next page of a module you can use the left and right arrows (they look a bit like this < and >). Depending on your screen size they will either appear at the bottom of each page, or on the left and right hand sides.

At the beginning of each module a set of learning objectives is provided in a blue box like this one.

Notes and useful additional information will be included green boxes.

Critical information may be provided in red boxes.

Exercises

Exercises for you to complete are included in yellow boxes. Exercises will sometimes include drop-down tasks, hints and solutions.

Tasks

Tasks will appear like this.

Hints

Hints will appear like this.

Solution

Solutions will appear like this.

R code and console output will be included in code blocks with an <R> symbol. You can copy/paste the code directly into R by hovering over the top right corner and clicking the button that appears.

# this code adds two numbers and stores the result
a = 1
b = 2
c = a + b

Any code outputs that would be printed to console will be displayed in code blocks with a an <output> symbol.

[1] "like this"