Untargeted metabolomics data for pooled human plasma sample
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 120
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Xian Fu
PROVIDER: MSV000096364 | MassIVE | Sat Nov 09 04:36:00 GMT 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:A pooled plasma of patients with chronic kidney disease and healthy controls analyzed by 13 individual CEs and stepped NCE 20/40/60% across 4 modes.
2024-11-09 | MSV000096364 | GNPS
Project description:Hydroxyapatite (HA) has significant clinical promise for the repair of bone defects and the modification of implant material interfaces. However, after implantation, there are potential risks of chronic inflammation. Dendritic cells (DCs) are key cells in regulating chronic inflammatory responses, and their phenotype and functions are influenced by the surface structure of materials. Therefore, in order to provide some theoretical guidance for the optimal design of HA surface structures, this study tried to construct stepped structures on HA surfaces and investigate the effects of stepped structures on the cytoskeletal, cellular morphology, and mRNA expression profile of immature dendritic cells (imDCs). HA dishes with stepped structures were prepared utilizing the principle of oriented attachment growth, and subsequently used to construct in vitro cell culture models. The imDCs were observed by immunofluorescence staining to characterize their cytoskeleton structures and cellular morphology. Besides, transcriptome sequencing was used to examine the changes in the mRNA expression profile of imDCs. The results indicated that the stepped structures exposed on HA surfaces would increase the spread area of imDCs and affect the cell adhesion morphology. In addition, the results of the transcriptome sequencing revealed significant alterations in the mRNA expression profile, with differentially expressed genes (DEGs) predominantly enriched in the pathways associated with the focal adhesion signal pathway, the chemokine signal pathway, and the IL-17 signal pathway. Thus, the stepped structures could modulatethe cellular morphology and the immunological functions of imDCs by modulating the aforementioned signal pathways, including the focal adhesion pathway, the chemokine signaling pathway, and the IL-17 signaling pathway, thereby affecting the immune response process.
2024-06-14 | GSE269464 | GEO
Project description:Lipidomics is a rapidly developing field in modern biomedical research. While LC-MS systems are able to detect most of the known lipid classes in a biological matrix, there is no single technique able to extract all of them simultaneously. In comparison with two-phase extractions, one-phase extraction systems are of particular interest, since they decrease the complexity of the experimental procedure. By using an untargeted lipidomics approach, we explored the differences/similarities between the most commonly used two-phase extraction systems (Folch, Bligh and Dyer, and MTBE) and one of the more recently introduced one-phase extraction systems for lipid analysis based on the MMC solvent mixture (MeOH/MTBE/CHCl3). The four extraction methods were evaluated and thoroughly compared against a pooled extract that qualitatively and quantitatively represents the average of the combined extractions. Our results show that the lipid profile obtained with the MMC system displayed the highest similarity to the pooled extract, indicating that it was most representative of the lipidome in the original sample. Furthermore, it showed better extraction efficiencies for moderate and highly apolar lipid species in comparison with the Folch, Bligh and Dyer, and MTBE extraction systems. Finally, the technical simplicity of the MMC procedure makes this solvent system highly suitable for automated, untargeted lipidomics analysis.
| S-EPMC6096717 | biostudies-literature
Project description:Plasma Cell-free DNA Sequencing data with human reads removed
| PRJNA865093 | ENA
Project description:The mechanisms of chronic kidney disease-associated secondary hyperparathyroidism are partially understood. In this project we aimed to gain new information and propose research hypotheses by proteome and phosphoproteome profiling of normal and hyperplastic rat parathyroid glands. Glands were microdissected from rats on normal control diet or CKD-inducing high adenine diet enriched with phosphorus to produce secondary hyperparathyroidism. Protein extracts were pooled from 12 glands (6 rats) for phosphoproteome profiling (3 normal and 3 CKD pools).
2022-06-28 | PXD029401 | Pride
Project description:Urine provides a diverse source of information related to health status and is ideal for clinical proteomics because of its ease of collection. To date, there is no standard operating procedure for reproducible and robust urine sample processing for mass spectrometry-based clinical proteomics. To address this need, a novel workflow was developed based on an on-bead protein capture, clean up, and digestion without the requirement from pre-processing steps such as precipitation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample were subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using a novel urine-HILIC (uHLC) approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analysed by LCMS in DIA mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. Data was searched in Spectronaut™ 17. Following statistical analysis, candidate protein markers were filtered at ≥ 2-fold change in abundance, ≥ 2 uniques peptides and ≤ 1% false discovery rate. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method. With fewer manuel processiing steps, a lower peptide and protein CV was observed in the uHLC technical replicates. Analysis of clinical samples revealed many significant, differentially abundant kidney injury-associated urinary proteins. The pilot data derived using this novel workflow provides information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
2024-01-26 | PXD043925 | Pride
Project description:Lyophilization is a common method used for stabilizing biological samples prior to storage or to concentrate extracts. However, it is possible that this process may alter the metabolic composition or lead to the loss of metabolites. In this study, the performance of lyophilization is investigated in the example of wheat roots. To this end, native and 13C-labelled, fresh or already lyophilized root samples, and (diluted) extracts with dilution factors up to 32 and authentic reference standards were investigated. All samples were analyzed using RP-LC-HRMS. Results show that using lyophilization for the stabilization of plant material altered the metabolic sample composition. Overall, 7% of all wheat metabolites detected in non-lyophilized samples were not detected in dried samples anymore, and up to 43% of the remaining metabolites exhibited significantly increased or decreased abundances. With respect to extract concentration, less than 5% of the expected metabolites were completely lost by lyophilization and the recovery rates of the remaining metabolites were slightly reduced with increasing concentration factors to an average of 85% at an enrichment factor of 32. Compound annotation did not indicate specific classes of wheat metabolites to be affected.
| S-EPMC10300689 | biostudies-literature
Project description:We investigated the endogenous peptidomes of spent hemodialysate, urine, and plasma, to shed light on peptide handling in the kidney. Our study was based on the hypothesis that hemodialysis replaces glomerular filtration and aims at gaining first insight into the comparative distribution of the peptidome/proteome in these body fluids. These data are expected to support insight into the underlying biological and physiological processes that take place in the kidney, which may help to advance treatment in advanced-stage chronic kidney disease and detoxification in renal replacement therapies.
2020-07-31 | PXD019407 | Pride
Project description:Kidney physiology has diurnal variation and abnormal circadian rhythm is associated with kidney disease. However, it is not known whether glomeruli, the filtering units in the kidney, are under circadian control. We therefore investigated core circadian clock components in glomeruli, together with their rhythmic targets and modes of regulation.
2024-09-20 | E-MTAB-13457 | biostudies-arrayexpress