Project description:The data set contains MS/MS data on teeth extracts for Ancient DNA teeth samples ran in both positive and Negative ionization modes
Project description:Seeds of Arabidopsis thaliana wild type and knockout-mutants for flavonoid genes (tt7 [3 lines], fls1, tt3, tt4, tt7tt4 [2 lines] ) were subjected to untargeted metabolomic analyses (LC-MS/MS) in positive and negative ionisation mode.
Project description:Secondary metabolite profiles of Aspergillus fumigatus aneuploids, WT, and nscROE strains under FK506 stress. Data include both positive and negative ionization modes from a 25-minute reverse-phase run conducted in 2025.
Project description:<p>Gallbladder cancer (GBC) is an aggressive malignancy often associated with gallstones (GBCGS), a condition distinct from gallstone disease (GSD). Both GBC and GBCGS are rare, with unclear pathogenesis and no established biomarker-based solutions. This pilot study aimed to identify distinct metabolic signatures in GBC and GBCGS for early diagnosis and stratification of high-risk GSD patients. A comparative untargeted serum metabolomic profiling was performed across three patient groups: GBC (n1=9), GBCGS (n2=11), and GSD (n3=10). A total of 35,385 mass-features in both positive and negative ionization modes with MS/MS characteristics were detected and annotated into 736 biochemicals.</p>
Project description:Punarnava [Boerhaavia diffusa L.] is a medicinal plant and constituent of several Indian traditional medicines. According to Ayurveda, this plant is a rich source of nutrients. Traditionally, it is used to provide relief against various gastrointestinal disorders, treat wounds, reduce joint pains, and as an anti-stress agent. Despite its pharmacological importance, detailed characterization of the metabolite composition of this plant has not been reported to date. Therefore, we have taken up metabolomic profiling of Punarnava choorna, as part of a larger project of metabolomic profiling of ayurvedic drugs. We carried out a global metabolomic analysis using a high-resolution mass spectrometry to investigate metabolite composition of Punarnava choorna. In total 1747 and 4031 features were identified at MS1 using XCMS in the positive and negative modes, respectively. Using MS2Compound, we identified 1229 and 709 features in the positive and negative modes, respectively. We also identified 362 and 191 metabolites at MS2 level in the positive and negative modes, respectively using the MS2Compound tool. The data were searched against the PlantCyc, KEGG, PhenolExplorer and HMDB databases. A large number of nutritionally important metabolites including amino acids, sugars and vitamins were identified in Purnarnava choorna. Further, the identified metabolites were mapped to their potential protein interactors using BindingDB tool. Highest number of interactions was observed for plant serotonins. The data provides molecular evidence to accelerate the discovery of mode of action of Purnarnava choorna.
Project description:Background: Renal dysfunction is a common and serious complication in patients with end-stage liver diseases. While some patients recover renal function after liver transplantation (LT), others do not. Additionally, patients with normal kidney function (Normal-KF) before LT may develop post-transplant renal dysfunction. Early identification of patients at risk for impaired kidney function (Impaired-KF) post-LT is critical to improving outcomes. This study integrated metabolomic and proteomic analyses to investigate molecular profiles distinguishing Normal-KF from Impaired-KF post-LT. Methods: Nine LT recipients were classified into Normal-KF (n=5) and Impaired-KF (n=4) groups. One additional recipient with pre-transplant renal function impairment who recovered renal function after LT, was analyzed separately. Plasma samples were collected at 2- and 5-weeks post-LT. The metabolomic and proteomic profiles were assessed by untargeted liquid chromatography-tandem mass spectrometry. Results: Metabolomic analysis identified 29 significantly altered metabolites between Normal-KF and Impaired-KF (fold change>2, p<0.05). Proteomic analysis revealed 45 differentially expressed proteins (fold change>1.25, p<0.05). For the recovered patient, the metabolomic profile closely resembled Normal-KF, whereas the proteomic profile remained aligned with Impaired-KF at both 14- and 35-days post-LT. From week 2 to week 5, both the metabolomic and proteomic profiles of the recovered patient showed trends toward the Normal-KF. Conclusion: This study revealed distinct metabolomic and proteomic signatures associated with renal dysfunction post-LT. Proteomic profiles indicated a delayed recovery compared to metabolomic profiles, suggesting a dynamic and muti-layered renal recovery process. Further research is warranted to elucidate the functional implications of the differential proteins and metabolites for improved monitoring and therapeutic strategies.
Project description:<p>The epididymis is the primary organ responsible for sperm maturation, with its caudal region serving as the primary storage site for mature sperm. The unique small molecule metabolites present in the cauda epididymal fluid not only facilitate the long-term storage of sperm but also ensure their structural and functional integrity prior to fertilization. Consequently, an in-depth investigation into the composition and functions of these metabolites in the cauda epididymal fluid is essential for elucidating the regulatory mechanisms governing sperm maturation and fertilization. Yaks, as livestock unique to the Qinghai-Tibet Plateau, hold significant scientific and economic value. Compared to cattle, male yaks exhibit poorer reproductive performance, characterized by reduced sperm motility, elevated sperm abnormality rate, and lower artificial insemination conception rates. To investigate the relationship between sperm motility defects in yaks and the microenvironment during their maturation, this study collected cauda epididymal fluid from yaks and cattle for untargeted metabolomic sequencing. The results indicated that 1,098 and 1,297 kinds of metabolites annotated by the Human Metabolome Database (HMDB) database were identified in yak and cattle cauda epididymal fluid, respectively, using positive and negative ion modes. In both modes, the three categories containing the most types of metabolites were organic acids and derivatives, organoheterocyclic compounds, and lipids and lipid-like molecules. Within the lipid metabolites, fatty acids and conjugates were the most prevalent in both modes. In the positive ion mode, compared to cattle cauda epididymal fluid, 79 metabolites were significantly upregulated and 212 were significantly downregulated in yak cauda epididymal fluid. In the negative ion mode, compared to cattle cauda epididymal fluid, 110 metabolites were significantly upregulated and 230 metabolites were significantly downregulated in yak cauda epididymal fluid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment results showed that the most significantly enriched pathway in the positive ion mode was the biosynthesis of amino acids, while in the negative ion mode, it was ABC transporters. Among the significant differentially expressed metabolites, 18 have been associated with sperm mobility, maturation or function. The functions of these metabolites involve regulation of oxidative stress, sperm capacitation, spontaneous acrosome reaction, mitochondrial energy metabolism, mRNA methylation, and flagellar motility. Taken together, these findings establish a foundational dataset and offer novel perspectives for elucidating the molecular mechanisms underlying yak sperm maturation, enhancing sperm motility, optimizing reproductive techniques, and ultimately improving reproductive performance.</p>