Project description:This dataset presents a detailed lipidomics analysis of single bacterial strains from the Oligo-Mouse-Microbiota (OMM12) model, cultured in vitro, using high-resolution mass spectrometry in ESI negative (ESI-) mode.
Project description:Lipid alterations in the brain have been implicated in many neurodegenerative diseases. To facilitate comparative lipidomic research across brain diseases here we establish a data common named the Neurolipid Atlas, that we have pre-populated with isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. Additionally, the resource contains lipidomics data of human and mouse brain tissue. Leveraging multiple datasets, we demonstrate that iPSC-derived neurons, microglia, and astrocytes exhibit distinct lipid profiles that recapitulate in vivo lipotypes. Notably, the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation specifically in human astrocytes, and we also observe CE accumulation in whole human AD brain lipidomics. Multi-omics interrogation of iPSC-derived astrocytes revealed that altered cholesterol metabolism plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex class I antigen presentation. Our data commons, available at neurolipidatlas.com, and allows for data deposition by the community and provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.
Project description:Established bacterial proteome sample preparations, including sonication and bead beating, leave insoluble carbohydrate-rich cell envelope pellets with an abundance of vital proteins often overlooked or missed in LC-MS/MS analyses. Triflic acid selectively removes glycans and we demonstrate that in comparison to sonication alone, incubation of whole bacterial cells as well as post-sonication insoluble pellets yields membrane and cell envelope-associated proteins for LC-MS/MS detection. We provide a detailed side-by-side comparison of triflic acid and sonication preparations for Gram- (Pseudomonas aeruginosa), Gram+ (Bacillus subtilis), and a complex bacterial human distal gut microbiome sample. Further, human Jurkat cells that lack a peptidoglycan and are readily solubilized by established methods, reveal only subtle differences in measurable proteins by LC-MS/MS between sonication and triflic acid preparations. Critically, we show that our new triflic acid-based proteome preparation method is broadly applicable and greatly improves our ability to detect and quantitate bacterial cell envelope proteins.
Project description:Here we present the development and application of LC-FAIMS-MS/MS based platform for untargeted lipidomics. The combination of normal phase liquid chromatography (NPLC), which can separate different types of phospholipids based on their head groups, and high-resolution MS (HRMS) offers a powerful qualitative and quantitative workflow for serum lipid profiling.We exploited this NPLC-FAIMS-HRMS to analyze the serum lipid profiles in mice infected intranasally with Acinetobacter baumannii, and developed an MS/MS matching tool to identify the detected lipids.
Project description:Lipidomics, proteomics and metabolomics characterization of the ontogeny of lipid, protein and metabolite changes during normal postnatal lung development