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Metabolomics

, Volume 10, Issue 6, pp 1084–1093 | Cite as

MetaboNexus: an interactive platform for integrated metabolomics analysis

  • Shao-Min Huang
  • Weizhong Toh
  • Peter Imre Benke
  • Chuen Seng Tan
  • Choon Nam Ong
Software/Database Article

Abstract

MetaboNexus is an interactive metabolomics data analysis platform that integrates pre-processing of raw peak data with in-depth statistical analysis and metabolite identity search. It is designed to work as a desktop application hence uploading large files to web servers is not required. This could speed up the data analysis process because server queries or queues are avoided, while ensuring security of confidential clinical data on a local computer. With MetaboNexus, users can progressively start from data pre-processing, multi- and univariate analysis to metabolite identity search of significant molecular features, thereby seamlessly integrating critical steps for metabolite biomarker discovery. Data exploration can be first performed using principal components analysis, while prediction and variable importance can be calculated using partial least squares-discriminant analysis and Random Forest. After identifying putative features from multi- and univariate analyses (e.g. t test, ANOVA, Mann–Whitney U test and Kruskal–Wallis test), users can seamlessly determine the molecular identity of these putative features. To assist users in data interpretation, MetaboNexus also automatically generates graphical outputs, such as score plots, diagnostic plots, boxplots, receiver operating characteristic plots and heatmaps. The metabolite search function will match the mass spectrometric peak data to three major metabolite repositories, namely HMDB, MassBank and METLIN, using a comprehensive range of molecular adducts. Biological pathways can also be searched within MetaboNexus. MetaboNexus is available with installation guide and tutorial at http://www.sph.nus.edu.sg/index.php/research-services/research-centres/ceohr/metabonexus, and is meant for the Windows Operating System, XP and onwards (preferably on 64-bit). In summary, MetaboNexus is a desktop-based platform that seamlessly integrates the entire data analytical workflow and further provides the putative identities of mass spectrometric data peaks by matching them to databases.

Keywords

Metabolomics Raw data pre-processing Statistical analysis Software Mass spectrometry Feature selection 

Notes

Acknowledgments

SM Huang was supported by an NUS Research Scholarship. We thank the Singapore National Medical Research Council (NMRC 1242/2009 WBS R-608-000-034-213) and the NUS Environmental Research Institute (NERI) for the support of this work.

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Shao-Min Huang
    • 1
  • Weizhong Toh
    • 1
  • Peter Imre Benke
    • 2
  • Chuen Seng Tan
    • 1
  • Choon Nam Ong
    • 1
    • 2
  1. 1.Saw Swee Hock School of Public HealthNational University of Singapore (NUS)SingaporeSingapore
  2. 2.National University of Singapore Environmental Research Institute (NERI)SingaporeSingapore

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