We report a method that enables automated data-dependent acquisition of lipid tandem mass spectrometry data in parallel with a high-resolution mass spectrometry imaging experiment. The method does not increase the total image acquisition time and is combined with automatic structural assignments. This lipidome-per-pixel approach automatically identified and validated 104 unique molecular lipids and their spatial locations from rat cerebellar tissue.
Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in ”database table format” which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.
A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.
Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.
Giant unilamellar vesicles (GUVs) are simple model membrane systems of cell-size, which are instrumental to study the function of more complex biological membranes involving heterogeneities in lipid composition, shape, mechanical properties, and chemical properties. We have devised a method that makes it possible to prepare a uniform sample of ternary GUVs of a prescribed composition and heterogeneity by mixing different populations of small unilamellar vesicles (SUVs). The validity of the protocol has been demonstrated by applying it to ternary lipid mixture of DOPC, DPPC, and cholesterol by mixing small unilamellar vesicles (SUVs) of two different populations and with different lipid compositions. The compositional homogeneity among GUVs resulting from SUV mixing is quantified by measuring the area fraction of the liquid ordered-liquid disordered phases in giant vesicles and is found to be comparable to that in GUVs of the prescribed composition produced from hydration of dried lipids mixed in organic solvent. Our method opens up the possibility to quickly increase and manipulate the complexity of GUV membranes in a controlled manner at physiological buffer and temperature conditions. The new protocol will permit quantitative biophysical studies of a whole new class of well-defined model membrane systems of a complexity that resembles biological membranes with rafts.
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