Bioinformatics and computational methods for lipidomics

Niemelä, Perttu; Castillo, Sandra; Sysi-Aho, Marko; Orešič, Matej

doi:10.1016/j.jchromb.2009.01.025

Cited by 89 publications

(53 citation statements)

References 107 publications

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“…It is advanced by the rapid development of sensitive and high resolution of mass spectrometry as well as lipid identification database, which allows for high-throughput analysis and accurate lipid profiling (Yamada et al, 2013). Processing of lipidomic data can also be achieved with the development of bioinformatics (Niemelä et al, 2009), and data could be visualized in multiple ways, such as principle component analysis plot and heat map, which enables sample classifications and a holistic overview (Bromke et al, 2015). However, the problem is the separation efficiency and ionization of various lipid classes, which could not be fully achieved by ultra-high performance liquid chromatography.…”

Section: Lipidomics For Diatom Lipid Analysismentioning

confidence: 99%

Exploring Valuable Lipids in Diatoms

et al. 2017

Front. Mar. Sci.

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Diatoms are one major group of algae in oceans that accounts almost half of marine primary food production and have also been identified as a promising candidate for biofuel production for their high level accumulation of lipids. They have gained increasingly attention for their potential applications in pharmaceuticals, cosmetics, nutrient supplements, and biofuels. This review aims to summarize the recent advances in diatom lipid study. Chemical structures and bioactivities of different lipid classes are discussed with a focus on valuable lipids such as fatty acids, polar lipids, steroids, and oxylipins from various diatoms species. Further, current extraction and fractionation approaches are compared and recent analytical techniques and methods are also reviewed with an emphasis on lipid class composition and fatty acid profiling. Biosynthetic pathways and key catalyzing enzymes are illustrated for a better understanding of fatty acid metabolism. Past engineering attempts toward generating appropriate diatom strains for lipid production are discussed with examples using mutagenesis, environmental stimulants, and genetic modification methods. Some possible future directions and applications of diatom-derived lipids are also proposed.

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Section: Lipidomics For Diatom Lipid Analysismentioning

confidence: 99%

Exploring Valuable Lipids in Diatoms

et al. 2017

Front. Mar. Sci.

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“…This suggests that the spatial intensity distribution reflects relative concentration differences of the lipid and fatty acid compounds in the spinal cord tissue. The "butterfly" shape of the gray matter in the spinal cord cross section was resolved in the corresponding ion images, indicating that a lateral [1,2], coupled with the availability of new and more powerful analytical methods of characterizing compounds of this diverse class [3,4], has propelled the rapid recent growth of the field of lipidomics [5][6][7]. The diverse functions of lipids include maintaining an electrochemical gradient, subcellular partitioning, cell signaling, energy storage, and membrane anchoring [2].…”

mentioning

confidence: 99%

Desorption electrospray ionization imaging mass spectrometry of lipids in rat spinal cord

Girod

Shi

Cheng

et al. 2010

J. Am. Soc. Mass Spectrom.

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Imaging mass spectrometry allows for the direct investigation of tissue samples to identify specific biological compounds and determine their spatial distributions. Desorption electrospray ionization (DESI) mass spectrometry has been used for the imaging and analysis of rat spinal cord cross sections. Glycerophospholipids and sphingolipids, as well as fatty acids, were detected in both the negative and positive ion modes and identified through tandem mass spectrometry (MS/MS) product ion scans using collision-induced dissociation and accurate mass measurements. Differences in the relative abundances of lipids and free fatty acids were present between white and gray matter areas in both the negative and positive ion modes. DESI-MS images of the corresponding ions allow the determination of their spatial distributions within a cross section of the rat spinal cord, by scanning the DESI probe across the entire sample surface. Glycerophospholipids and sphingolipids were mostly detected in the white matter, while the free fatty acids were present in the gray matter. These results show parallels with reported distributions of lipids in studies of rat brain. This suggests that the spatial intensity distribution reflects relative concentration differences of the lipid and fatty acid compounds in the spinal cord tissue. The "butterfly" shape of the gray matter in the spinal cord cross section was resolved in the corresponding ion images, indicating that a lateral resolution of better than 200 m was achieved. The selected ion images of lipids are directly correlated with anatomic features on the spinal cord corresponding to the white and the gray

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“…• Bioinformatics and computational methods for lipidomics [70]. This study dates back to 2009 and was one of the earlier studies highlighting the importance of computational support in areas for which over seven years later no general solutions have been provided.…”

Section: Lipid Databases and Bioinformaticsmentioning

confidence: 99%

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks

Pauling

Klipp

2016

Journal of Integrative Bioinformatics

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SummaryLipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

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Bioinformatics and computational methods for lipidomics

Cited by 89 publications

References 107 publications

Exploring Valuable Lipids in Diatoms

Exploring Valuable Lipids in Diatoms

Desorption electrospray ionization imaging mass spectrometry of lipids in rat spinal cord

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks

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