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Bioinformatics in Lipidomics: Automating Large-Scale LC-MS-Based Untargeted Lipidomics Profiling with SimLipid Software

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Plant Metabolic Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2396))

Abstract

Liquid chromatography–mass spectrometry (LC-MS) provides one of the most popular platforms for untargeted plant lipidomics analysis (Shulaev and Chapman, Biochim Biophys Acta 1862(8):786–791, 2017; Rupasinghe and Roessner, Methods Mol Biol 1778:125–135, 2018; Welti et al., Front Biosci 12:2494–506, 2007; Shiva et al., Plant Methods 14:14, 2018). We have developed SimLipid software in order to streamline the analysis of large-volume datasets generated by LC-MS-based untargeted lipidomics methods. SimLipid contains a customizable library of lipid species; graphical user interfaces (GUIs) for visualization of raw data; the identified lipid molecules and their associated mass spectra annotated with fragment ions and parent ions; and detailed information of each identified lipid species all in a single workbench enabling users to rapidly review the results by examining the data for confident identifications of lipid molecular species. In this chapter, we present the functionality of the software and workflow for automating large-scale LC-MS-based untargeted lipidomics profiling.

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Acknowledgments

The authors want to thank Ms. Himani Gupta, Sr. Bioinformatics Analyst, and Dr. Rajesh Pujari, Sr. Bioinformatics Analyst at PREMIER Biosoft for their contribution in performing the data analysis. SimLipid software is a property of PREMIER Biosoft(www.premierbiosoft.com), and the organization has sole ownership of the software IP. The article was written when the corresponding author was an employee of the organization and he is no longer associated with the organization. 

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Authors and Affiliations

  1. PREMIER Biosoft, Indore, India

    Ningombam Sanjib Meitei

  2. PREMIER Biosoft, Palo Alto, USA

    Ningombam Sanjib Meitei

  3. Department of Biological Sciences and Advanced Environmental Research Institute, University of North Texas, Denton, TX, USA

    Vladimir Shulaev

Authors
  1. Ningombam Sanjib Meitei
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  2. Vladimir Shulaev
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Editors and Affiliations

  1. Department of Biological Sciences, University of North Texas, Denton, TX, USA

    Vladimir Shulaev

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Meitei, N.S., Shulaev, V. (2022). Bioinformatics in Lipidomics: Automating Large-Scale LC-MS-Based Untargeted Lipidomics Profiling with SimLipid Software. In: Shulaev, V. (eds) Plant Metabolic Engineering. Methods in Molecular Biology, vol 2396. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1822-6_15

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  • DOI: https://doi.org/10.1007/978-1-0716-1822-6_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1821-9

  • Online ISBN: 978-1-0716-1822-6

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