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.