LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms

Ronny Herzog1, Dominik Schwudke2, Andrej Shevchenko3

1 Lipotype GmbH, Dresden, 2 Research Center Borstel, Borstel, Germany, 3 MPI of Molecular Cell Biology and Genetics, Dresden
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.12
DOI:  10.1002/0471250953.bi1412s43
Online Posting Date:  October, 2013
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LipidXplorer is an open‐source software kit that supports the identification and quantification of molecular species of any lipid class detected by shotgun experiments performed on any mass spectrometry platform. LipidXplorer does not rely on a database of reference spectra: instead, lipid identification routines are user defined in the declarative molecular fragmentation query language (MFQL). The software supports batch processing of multiple shotgun acquisitions by high‐resolution mass mapping, precursor and neutral‐loss scanning, and data‐dependent MS/MS lending itself to a variety of lipidomics applications in cell biology and molecular medicine. Curr. Protoc. Bioinform. 43:14.12.1‐14.12.30. © 2013 by John Wiley & Sons, Inc.

Keywords: mass spectrometry; shotgun lipidomics; MS/MS; LipidXplorer; lipid identification; lipid quantification; lipidomics screen

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Table of Contents

  • Introduction
  • Strategic Planning: Supported File Formats
  • Basic Protocol 1: Installing LipidXplorer
  • Support Protocol 1: File Conversion Using MSConvert
  • Basic Protocol 2: Basic Lipid Identification Workflow
  • Basic Protocol 3: Composing MFQL Queries for Top‐Down Shotgun Lipidomics
  • Basic Protocol 4: Composing MFQL Queries for Bottom‐Up Shotgun Lipidomics
  • Basic Protocol 5: Composing MFQL Queries for Lipid Identification by Neutral Loss Fragments
  • Basic Protocol 6: Troubleshooting Lipid Identifications
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
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