Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease.

Journal Article (Journal Article)

Mass spectrometry-based metabolomics has undergone significant progresses in the past decade, with a variety of software packages being developed for data analysis. However, systematic comparison of different metabolomics software tools has rarely been conducted. In this study, several representative software packages were comparatively evaluated throughout the entire pipeline of metabolomics data analysis, including data processing, statistical analysis, feature selection, metabolite identification, pathway analysis, and classification model construction. LC-MS-based metabolomics was applied to preclinical Alzheimer's disease (AD) using a small cohort of human cerebrospinal fluid (CSF) samples (N = 30). All three software packages, XCMS Online, SIEVE, and Compound Discoverer, provided consistent and reproducible data processing results. A hybrid method combining statistical test and support vector machine feature selection was employed to screen key metabolites, achieving a complementary selection of candidate biomarkers from three software packages. Machine learning classification using candidate biomarkers generated highly accurate and predictive models to classify patients into preclinical AD or control category. Overall, our study demonstrated a systematic evaluation of different MS-based metabolomics software packages for the entire data analysis pipeline which was applied to the candidate biomarker discovery of preclinical AD.

Full Text

Duke Authors

Cited Authors

  • Hao, L; Wang, J; Page, D; Asthana, S; Zetterberg, H; Carlsson, C; Okonkwo, OC; Li, L

Published Date

  • June 18, 2018

Published In

Volume / Issue

  • 8 / 1

Start / End Page

  • 9291 -

PubMed ID

  • 29915347

Pubmed Central ID

  • PMC6006240

Electronic International Standard Serial Number (EISSN)

  • 2045-2322

Digital Object Identifier (DOI)

  • 10.1038/s41598-018-27031-x


  • eng

Conference Location

  • England