Metabolomics Data Preprocessing Using ADAP and MZmine 2

Xiuxia Du*, Aleksandr Smirnov, Tomáš Pluskal, Wei Jia, Susan Sumner

*Corresponding author for this work

Research output: Chapter in book/report/conference proceedingChapterpeer-review

36 Citations (Scopus)


The informatics pipeline for making sense of untargeted LC–MS or GC–MS data starts with preprocessing the raw data. Results from data preprocessing undergo statistical analysis and subsequently mapped to metabolic pathways for placing untargeted metabolomics data in the biological context. ADAP is a suite of computational algorithms that has been developed specifically for preprocessing LC–MS and GC–MS data. It consists of two separate computational workflows that extract compound-relevant information from raw LC–MS and GC–MS data, respectively. Computational steps include construction of extracted ion chromatograms, detection of chromatographic peaks, spectral deconvolution, and alignment. The two workflows have been incorporated into the cross-platform and graphical MZmine 2 framework and ADAP-specific graphical user interfaces have been developed for using ADAP with ease. This chapter summarizes the algorithmic principles underlying key steps in the two workflows and illustrates how to apply ADAP to preprocess LC–MS and GC–MS data.

Original languageEnglish
Title of host publicationComputational Methods and Data Analysis for Metabolomics
EditorsShuzhao Li
Place of PublicationNew York
PublisherHumana Press Inc.
Number of pages24
ISBN (Electronic)9781071602393
ISBN (Print)9781071602386, 9781071602416
Publication statusPublished - 18 Jan 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Scopus Subject Areas

  • Molecular Biology
  • Genetics

User-Defined Keywords

  • ADAP
  • Alignment
  • Data preprocessing
  • GC–MS
  • LC–MS
  • Metabolomics
  • MZmine 2
  • Peak picking
  • Spectral deconvolution
  • Visualization


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