@inbook{e75b2a89f3c1406f9c9b3b5521eeb14c,
title = "Metabolomics Data Preprocessing Using ADAP and MZmine 2",
abstract = "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.",
keywords = "ADAP, Alignment, Data preprocessing, GC–MS, LC–MS, Metabolomics, MZmine 2, Peak picking, Spectral deconvolution, Visualization",
author = "Xiuxia Du and Aleksandr Smirnov and Tom{\'a}{\v s} Pluskal and Wei Jia and Susan Sumner",
note = "Funding Information: We thank the USA National Science Foundation award 1262416 and National Institutes of Health/National Cancer Institute grant U01CA235507 for funding the research and development of ADAP.",
year = "2020",
month = jan,
day = "18",
doi = "10.1007/978-1-0716-0239-3_3",
language = "English",
isbn = "9781071602386",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "25--48",
editor = "Shuzhao Li",
booktitle = "Computational Methods and Data Analysis for Metabolomics",
edition = "1st",
}