This document contains notes for metabolomics and chemoinformatics. It is a personal notebook, therefore it was not structured in a logic manner and some contents might be redundant while some are over-simplified.

You are welcome to read it if you find some parts useful. Please keep in mind that this notebook was not designed to be read through in order. Use the sidebar to navigate to what you need.

Happy reading!


This notebook may contain a large variety of information on different mass spectrometers (MS). It by no means attempts to replace any official user manuals. Instead, it aims at providing the author (maybe some other users as well) a basic knowledge of understanding, operating and trouble-shooting of the MS. It is strongly recommended to read and follow the official user manuals before starting your very first experiment.

The author does not take any responsibility for the consequences caused by any mistakes in this notebook.

Writing style

The following styles are used in this notebook in order to improve the readability of this notebook.

  • Concepts are displayed by inline block, e.g., Metabolomics is defined as the comprehensive analysis of metabolites in a biological specimen.

  • Important statements are highlighted in bold, e.g., This is important .

  • Codes are shown in code block. e.g.,

a <- sqrt(10)
b <- a^2
  • Quotes are listed in quote block. e.g.,

“Be yourself; everyone else is already taken.”

  • Three types of blocks are used to show notes, tips and warnings:
Always be aware of what to do with, and the effect of, safety information
Be sure to read and comply with all precautions.
The source exhaust might contain noxious mayerials.
  • References are listed at the end of each chapter, e.g, This notebook was written by R package bookdown (Xie 2020).


The author would like to thank himself for not (yet) quitting writing this notebook.

This notebook was made possible thanks to the R package bookdown (Xie 2020).


Xie, Yihui. 2020. Bookdown: Authoring Books and Technical Documents with r Markdown.