MetaboAnalyst: a web server for metabolomic data analysis and interpretation

Abstract

Metabolomics is a newly emerging field of 'omics' research that is concerned with characterizing large numbers of metabolites using NMR, chromatography and mass spectrometry. It is frequently used in biomarker identification and the metabolic profiling of cells, tissues or organisms. The data processing challenges in metabolomics are quite unique and often require specialized (or expensive) data analysis software and a detailed knowledge of cheminformatics, bioinformatics and statistics. In an effort to simplify metabolomic data analysis while at the same time improving user accessibility, we have developed a freely accessible, easy-to-use web server for metabolomic data analysis called MetaboAnalyst. Fundamentally, MetaboAnalyst is a web-based metabolomic data processing tool not unlike many of today's web-based microarray analysis packages. It accepts a variety of input data (NMR peak lists, binned spectra, MS peak lists, compound/concentration data) in a wide variety of formats. It also offers a number of options for metabolomic data processing, data normalization, multivariate statistical analysis, graphing, metabolite identification and pathway mapping. In particular, MetaboAnalyst supports such techniques as: fold change analysis, t-tests, PCA, PLS-DA, hierarchical clustering and a number of more sophisticated statistical or machine learning methods. It also employs a large library of reference spectra to facilitate compound identification from most kinds of input spectra. MetaboAnalyst guides users through a step-by-step analysis pipeline using a variety of menus, information hyperlinks and check boxes. Upon completion, the server generates a detailed report describing each method used, embedded with graphical and tabular outputs. MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. MetaboAnalyst is accessible at http://www.metaboanalyst.ca.

Figure 1.

A diagram illustrating MetaboAnalyst's workflow and data processing options. Different data inputs are first transformed into compatible data matrices using several different processing methods. A variety of algorithms are implemented for data normalization, analysis, and annotation. The number of available options is shown inside the round brackets for each category. At the end of any given analysis, a comprehensive PDF report, the processed data, and high-resolution images are available for download.

Figure 2.

Examples of some of the graphical output and analyses available from MetaboAnalyst. (A) PLS-DA class separation based on the top three components. (B) Significant features identified by SAM analysis. (C) Heat map generated from hierarchical clustering. (D) Features ranked by random forest. The binned NMR spectral data (test data #2) was used to generate these graphs.