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Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
Published on: March 14, 2013
Protocol for untargeted LC-MS/MS metabolomics annotation and differential abundance analysis using the SIRIUS Python
Jonas A Emmert1, Sebastian Böcker2, Markus Fleischauer3
1Chair for Bioinformatics, Institute for Computer Science, Friedrich Schiller University Jena, Hans-Knöll-Straße 6, 07745 Jena, Thuringia, Germany; International Max Planck Research School "Chemical Communication in Ecological Systems", Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 6, 07745 Jena, Thuringia, Germany.
Abstract:
We present a protocol for programmatic untargeted LC-MS/MS metabolomics using PySirius, the Python client for SIRIUS. We describe steps for importing data with LC-MS feature alignment, and annotating features with molecular formulas, structures, and compound classes. We then detail procedures for analyzing differential abundance by fold change between groups and visualizing results. As proof of concept, we replicate the finding that rosmarinic acid is more abundant in old than young rosemary (Rosmarinus officinalis) leaves.
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