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LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

Jennifer E Kyle1, Kevin L Crowell1, Cameron P Casey1

  • 1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.

Bioinformatics (Oxford, England)
|February 4, 2017
PubMed
Summary

We developed LIQUID, an open-source software for processing lipidomics data from liquid chromatography-tandem mass spectrometry (LC-MS/MS). LIQUID offers faster processing and more validated lipid identifications compared to existing tools.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Mass Spectrometry

Background:

  • Lipidomics research generates large datasets requiring efficient data processing.
  • Accurate identification of lipid molecular species is crucial for biological interpretation.
  • Existing software for lipid identification has limitations in speed and validation.

Purpose of the Study:

  • To introduce LIQUID, an open-source software for semi-automated processing and visualization of LC-MS/MS lipidomics data.
  • To provide a user-friendly interface with customizable features for lipid identification.
  • To compare LIQUID's performance against other commonly used lipid identification software.

Main Methods:

  • Development of LIQUID with a graphical user interface.
  • Implementation of a customizable target library and scoring model.
  • Semi-automated processing and visualization of LC-MS/MS data.
  • Comparative analysis of LIQUID with CFM-ID, MetFrag, GNPS, LipidBlast, and MS-DIAL.

Main Results:

  • LIQUID enables semi-automated processing and visualization of high-throughput lipidomics data.
  • The software features a customizable target library and scoring model for project-specific needs.
  • LIQUID demonstrated faster processing times and a higher number of validated lipid identifications compared to benchmark software.
  • The graphical user interface facilitates confident identification of lipid molecular species through spectral evidence visualization.

Conclusions:

  • LIQUID is an effective open-source tool for LC-MS/MS-based lipidomics data analysis.
  • It offers advantages in processing speed and identification accuracy over existing software.
  • LIQUID facilitates confident lipid identification, aiding biological discovery in lipidomics research.