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Lipid-Pro: A Bioinformatics Tool for Rapid Identification of Lipids in Pre-processed DIA Data

Zeeshan Ahmed1, 2, 3, 4*, Michel Mayr5, Saman Zeeshan4, Thomas Dandekar4, Martin J. Mueller5 and Agnes Fekete5
  • 1 The Jackson Laboratory for Genomic Medicine, United States
  • 2 University of Massachusetts, School of Medicine, United States
  • 3 University of Wuerzburg, Department of Neurobiology and Genetics, Biocenter, Germany
  • 4 University of Wuerzburg, Department of Bioinformatics, Biocenter, Germany
  • 5 University of Wuerzburg, Department of Pharmaceutical Biology, Biocenter, Germany

Mass spectra of lipid species in complex biological samples are a challenge to interpret since the lipid composition is specific to organism, tissue and cell. Additionally, thousands of lipid species are present in a biological sample and the number of lipid classes and the isomer are high and diverse. For their accurate identification different measured physicochemical properties, such as accurate mass, fragmentation behaviour and a polarity, have to be considered in the pre-processed data. Here, we present a recently proposed bioinformatics tool i.e. Lipid-Pro (Ahmed et al., 2015a; Ahmed et al., 2015b), a desktop application for the interpretation of LC-MS/MS data. It is a lipid identification solution towards the lipidome analysis, where defined lipid species are identified in the pre-processed data (lipid profiling). The graphical interface of the Lipid-Pro is very simple to install and use. It consists of five main modules: Building Bock, Precursor Candidates, Fragment Candidates, Mass Analyzer and Lipid Identifier. Using these modules, user can define building blocks, compose lipid molecular ions and their fragments, calculate m/z-values of lipid molecular ions and their characteristic fragments, and identify lipid species. Moreover, it also provide comprehensive data management, sharing and integration features. Lipid-Pro is a well-planned scientific solution, implementing the Butterfly paradigm (Ahmed et al., 2014a; Ahmed et al., 2014b). Started with the initialization of the finalized scientific solution’s requirements, then modelled and mocked using HCI guidelines. It is programmed in C# programming language, using Microsoft Dot Net Framework and only compatible to the Microsoft Windows Operating Systems (preferred OS version: 7). The most recent available version of Lipid-Pro has been tested and validated at the Metabolomics Core Unit and Department of Pharmaceutical Biology, University of Wuerzburg Germany. Lipid-Pro is a freely available tool for non-commercial, academic and scientific research, accessible at the following web link: (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/). To have complete application details, please consult publication (Ahmed et al., 2015a).

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Acknowledgements

Funding: The authors would like to thank German Research Foundation (DFG-CRC-SFB-1047 to ZA, MM, MJM, AF and DFG-CRC-TR34/Z1 to SZ, TD) for funding on this research.

Support: The authors thank to the University of Wuerzburg Germany, University of Massachusetts USA and The Jackson Laboratory for Genomic Medicine USA for support in this publication. Authors also thank to all interested colleagues for critical input on the approach and anonymous reviewers for helpful comments.

References

Ahmed, Z., Michel, M., Saman, Z., Dandekar, T., Mueller, M J., Fekete A. (2015a). Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics 31, 1150-1153.
Ahmed, Z., Dandekar, T., Mueller, M J., Fekete A. (2015b). Lipid-Pro: A Bioinformatics Tool towards Lipid Identification. In the proceedings of 11th Annual International Conference of the Metabolomics Society, the University of California, Davis, San Francisco Bay, USA.
Ahmed, Z., Saman, Z., Dandekar, T. (2014a). Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm. F1000Research 3, 71.
Ahmed, Z., Saman, Z. (2014b). Cultivating Software Solutions Development in the Scientific Academia. Rec Pat Comp Sci 7, 54-63.

Keywords: bioinformatics, Lipid-Pro, lipidomics, Mass spectra, Software

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Demo, to be considered for oral presentation

Topic: General neuroinformatics

Citation: Ahmed Z, Mayr M, Zeeshan S, Dandekar T, Mueller MJ and Fekete A (2015). Lipid-Pro: A Bioinformatics Tool for Rapid Identification of Lipids in Pre-processed DIA Data. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00023

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Received: 03 Mar 2015; Published Online: 05 Aug 2015.

* Correspondence: Dr. Zeeshan Ahmed, The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States, zahmed@ifh.rutgers.edu