LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

Michelle F. Clasquin1, Eugene Melamud2, Joshua D. Rabinowitz3

1 Molecular Biomarkers, Merck Research Laboratories, West Point, Pennsylvania, 2 Oncology, Pfizer, Pearl River, New York, 3 Department of Chemistry and Integrative Genomics, Carl Icahn Laboratory, Princeton, New Jersey
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.11
DOI:  10.1002/0471250953.bi1411s37
Online Posting Date:  March, 2012
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MAVEN is an open‐source software program for interactive processing of LC‐MS‐based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high‐resolution full‐scan mass spectrometry data. It automatically detects and reports peak intensities for isotope‐labeled metabolites. Menu‐driven, click‐based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step‐by‐step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope‐labeling patterns, and export of tables of metabolite‐specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC‐MS data into a form ready for biological analysis. Curr. Protoc. Bioinform. 37:14.11.1‐14.11.23. © 2012 by John Wiley & Sons, Inc.

Keywords: metabolomics; liquid chromatography‐mass spectrometry; pathway visualization and mapping; stable isotope labeling; metabolic flux analysis; kinetic flux profiling

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Loading LC‐MS Data into MAVEN
  • Basic Protocol 2: Peak Alignment and Visualization
  • Basic Protocol 3: Untargeted Analysis of Full‐Scan LC‐MS Data
  • Basic Protocol 4: Targeted Metabolite Quantitation
  • Basic Protocol 5: Targeted Analysis of Full‐Scan LC‐MS Data with Isotopic Labeling
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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