Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2022 Jan;17(1):129-151.
doi: 10.1038/s41596-021-00636-9. Epub 2021 Dec 24.

Optimization of metabolomic data processing using NOREVA

Affiliations
Review

Optimization of metabolomic data processing using NOREVA

Jianbo Fu et al. Nat Protoc. 2022 Jan.

Abstract

A typical output of a metabolomic experiment is a peak table corresponding to the intensity of measured signals. Peak table processing, an essential procedure in metabolomics, is characterized by its study dependency and combinatorial diversity. While various methods and tools have been developed to facilitate metabolomic data processing, it is challenging to determine which processing workflow will give good performance for a specific metabolomic study. NOREVA, an out-of-the-box protocol, was therefore developed to meet this challenge. First, the peak table is subjected to many processing workflows that consist of three to five defined calculations in combinatorially determined sequences. Second, the results of each workflow are judged against objective performance criteria. Third, various benchmarks are analyzed to highlight the uniqueness of this newly developed protocol in (1) evaluating the processing performance based on multiple criteria, (2) optimizing data processing by scanning thousands of workflows, and (3) allowing data processing for time-course and multiclass metabolomics. This protocol is implemented in an R package for convenient accessibility and to protect users' data privacy. Preliminary experience in R language would facilitate the usage of this protocol, and the execution time may vary from several minutes to a couple of hours depending on the size of the analyzed data.

PubMed Disclaimer

References

    1. Pareek, V., Tian, H., Winograd, N. & Benkovic, S. J. Metabolomics and mass spectrometry imaging reveal channeled de novo purine synthesis in cells. Science 368, 283–290 (2020). - PubMed - PMC - DOI
    1. Delzenne, N. M. & Bindels, L. B. Microbiome metabolomics reveals new drivers of human liver steatosis. Nat. Med. 24, 906–907 (2018). - PubMed - DOI
    1. Paschos, G. K. & FitzGerald, G. A. Circadian clocks and metabolism: implications for microbiome and aging. Trends Genet. 33, 760–769 (2017). - PubMed - PMC - DOI
    1. Wishart, D. S. Emerging applications of metabolomics in drug discovery and precision medicine. Nat. Rev. Drug Discov. 15, 473–484 (2016). - PubMed - DOI
    1. Edison, A. S. et al. NMR: unique strengths that enhance modern metabolomics research. Anal. Chem. 93, 478–499 (2021). - PubMed - DOI

Publication types

LinkOut - more resources