Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry data of human urine

ABSTRACT: Based on UPLC-Q-TOF-MS metabolomics technology, urine samples of 1072 subjects from 9 centers, including normal control, phlegm and blood stasis (PBS) syndrome and Qi and Yin deficiency (QYD) syndrome, and other syndromes of CHD, were conducted to find biomarkers. Among them, the discovery set (n = 125) and the test set (n = 337) were used to identify and validate biomarkers, and the validation set (n = 610) was used for the application and evaluation of the support vector machine (SVM) prediction model.

INSTRUMENT(S): Q-Tof ultima

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Yubo Li

LAB HEAD: Yubo Li

PROVIDER: PXD012910 | Pride | 2019-03-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DiscoverySet.7z	Other
	DiscoverySet.xlsx	Xlsx
	TestSet.7z	Other
	TestSet.xlsx	Xlsx
	ValidationSet1.7z	Other

Items per page:

1 - 5 of 8

Publications

A Large-Scale, Multi-Center Urine Biomarkers Identification of Coronary Heart Disease in TCM Syndrome Differentiation.

Zhou Haonan H Li Lin L Zhao Huan H Wang Yuming Y Du Jun J Zhang Pengjie P Li Chunjie C Wang Xianliang X Liu Yuechen Y Xu Qiang Q Zhang Tianpu T Song Yanqi Y Yu Chunquan C Li Yubo Y

Journal of proteome research 20190409 5

Coronary heart disease (CHD) threatens human health. The discovery and assessment of potential biometabolic markers for different syndrome types of CHD may contribute to decipher pathophysiological mechanisms and identify new targets for diagnosis and treatment. On the basis of UPLC-Q-TOF/MS metabolomics technology, urine samples of 1072 participants from nine centers, including normal control, phlegm and blood stasis (PBS) syndrome and Qi and Yin deficiency (QYD) syndrome, and other syndromes o ...[more]

PMID: 30907085

Similar Datasets

Acetylation changes in NQO1 overexpression in Mouse Skeletal Mucscle

Project description:In this manuscript we have explored the role of both Nrf2 and NQO1 in protection against diet-induced metabolic syndrome and demonstrate that both Nrf2 and NQO1 provide protection against HFD-induced adverse phenotypes in a mouse model

2021-09-08 | PXD015070 | Pride

Identification of a collagen marker in urine improves the detection of colorectal liver metastases

Project description:Previously, we reported that a combination of a collagen alpha-1(I) natural occurring peptide (NOP) AGPP(-OH)GEAGKP(-OH)GEQGVP(-OH)GDLGAP(-OH)GP (AGP) and serum carcinoembryonic antigen (CEA) has the potential to detect colorectal liver metastases (CRLM). The combined method needs to be adapted to increase the sensitivity and specificity before it can be implemented in the clinic. This mass spectrometry study aimed to identify additional collagen NOPs in urine to further increase the sensitivity and specificity of our previously published method and search for the most discriminating NOP panel. The new assay was developed based on urine samples from 100 healthy controls and 100 patients suffering from CRLM. Two additional NOPs were identified: GPPGEAGK(-OH)P(-OH)GEQGVP(-OH)GDLGAP(-OH)GP (GPP) originating from collagen alpha-1(I) and GNDGARGSDGQPGPP(-OH)GP(-OH)P(-OH)GTAGFP(-OH)GSP(-OH)GAK(-OH)GEVGP (GND) originating from collagen alpha-1(III). A molecular model combining NOPs (AGP, GPP, and GND) and CEA was generated. Molecules that did not contribute to the diagnostic power of the model were removed, resulting in a model only consisting of GND and CEA. In this model, 86% sensitivity and 84% specificity in the discovery set, and 92% sensitivity and 90% specificity in the validation set were reached. These percentages are significantly higher than the current model based on AGP and CEA (p=0.032). The performance of the new model is better than the currently used techniques in the clinic (e.g. CT-scan, ultrasound, serum CEA), which have a sensitivity between 57-70% and a specificity between 90-96%.

2019-11-15 | PXD013705 | Pride

Therapeutic Effects of Valeriana jatamansi on Ulcerative Colitis: Insights into Mechanisms of Action through Metabolomics and Microbiome Analysis

Project description:Ulcerative colitis (UC), belonging to inflammatory bowel disease (IBD), is a chronic and relapsing inflammatory disorders of the gastrointestinal tract, which is not completely cured so far. Valeriana jatamansi is a Chinese medicine used clinically to treat "diarrhea", which is closely related to UC. This study was to elucidate the therapeutic effects of V. jatamansi extract (VJE) on dextran sodium sulfate (DSS)-induced UC in mice and its underlying mechanism. In this work, VJE effectively ameliorate the symptoms, histopathological scores and reduce the production of inflammatory factors of UC mice. The colon untargeted metabolomics analysis and 16S rDNA sequencing showed remarkable differences in colon metabolite profiles and intestinal microbiome composition between the control and DSS groups, and VJE intervention can reduce these differences. Thirty-two biomarkers were found and modulated the primary pathways including pyrimidine metabolism, arginine biosynthesis and glutathione metabolism. Meanwhile, twelve significant taxa of gut microbiota were found. Moreover, there is a close relationship between endogenous metabolites and intestinal flora. These findings suggested that VJE ameliorates UC by inhibiting inflammatory factors, recovering intestinal maladjustment, and regulating the interaction between intestinal microbiota and host metabolites. Therefore, the intervention of V. jatamansi is a potential therapeutic treatment for UC.

2023-07-24 | PXD043047 | Pride

Lipases from Metagenomic Sources

Project description:Functional Metaproteomic approach was used to discover lipolytic enzymes.

2017-03-09 | PXD005148 | Pride

Epi-proteomic assessment of backpain therapy

Project description:This study investigates how molecular profiles evolve in response to standardized sport therapy and non-controlled lifestyle choices. We report that the therapy improves agility, attenuates backpain, and also triggers healthier habits. We find that a subset of participants´ histone methylation and acetylation profiles cluster samples according to their therapy status, before or after therapy. Integrating epigenetic reprogramming of both buccal cells and PBMCs reveals that these concomitant changes are concordant with higher levels of self-rated backpain improvement and agility gain. Additionally, epigenetic changes correlate with changes in immune-response plasma factors, reflecting their comparable ability to rate therapy effects at the molecular level. Additionally, we performed an exploratory analysis to confirm the usability of molecular profiles in 1) mapping lifestyle choices, and 2) evaluating the distance of a given participant to an optimal health state.

2024-10-21 | PXD050113 | Pride

Same same but different – The global response of Escherichia coli to five different LpxC inhibitors

Project description:A promising but yet clinically unexploited antibiotic target in difficult-to-treat Gram-negative bacteria is LpxC, the key enzyme in the biosynthesis of lipopolysaccharides (LPS), which are the major constituents of the outer membrane. To gain insights into the mode of action of five different LpxC inhibitors, we conducted a comparative phenotypic and proteomic analysis. All five compounds bound to purified LpxC from Escherichia coli. Treatment of E. coli with these compounds changed the cell shape and stabilized LpxC indicating that the inhibitor-bound enzyme is not degraded by the FtsH protease. LpxC inhibition sensitized E. coli to the cell wall antibiotic vancomycin, which typically does not cross the outer membrane. Four of the five compounds led to an accumulation of lyso-PE, a cleavage product of phosphatidylethanolamine (PE), generated by the phospholipase PldA. The combined results suggested an imbalance in phospholipid (PL) and LPS biosynthesis, which was corroborated by the global proteome response to treatment with the LpxC inhibitors. Apart from LpxC itself, FabA and FabB responsible for the biosynthesis of unsaturated fatty acids were consistently upregulated. Our work also shows that antibiotics targeting the same enzyme do not necessarily elicit identical cellular responses. Compound-specific marker proteins belonged to different functional categories, like stress responses, nucleotide or amino acid metabolism and quorum sensing. These findings provide new insights into common and distinct cellular defense mechanisms against LpxC inhibition. Moreover, they support a delicate balance between LPS and PL biosynthesis with great potential as point of attack for antimicrobial intervention.

2024-06-16 | PXD043195 | Pride

Integration of metabolomics and transcriptomics to reveal metabolic characteristics and key targets associated with cisplatin resistance in non-small cell lung cancer

Project description:Continuous exposure to cisplatin can induce drug resistance to limit efficacy, however, the underlying mechanisms correlated to cisplatin resistance are still unclear. Drug-sensitive A549 cells and cisplatin-resistant A549/DDP cells were used to explore the potential metabolic pathways and key targets associated with cisplatin resistance by integrating untargeted metabolomics with transcriptomics. The results of comprehensive analyses showed that 19 metabolites were significantly changed in A549/DDP vs A549 cells, and some pathways had a close relationship with cisplatin resistance, such as the biosynthesis of aminoacyl-tRNA, glycerophospholipid metabolism, and glutathione metabolism. Moreover, transcriptomics analysis showed glutathione metabolism was also obviously affected in A549/DDP, which indicated that glutathione metabolism played an import role in the process of drug resistance. Meanwhile, transcriptomics analysis suggested the four enzymes related to glutathione metabolism - CD13, GPX4, RRM2B, and OPLAH - as potential targets of cisplatin resistance in NSCLC. Further studies identified the over-expressions of these four enzymes in A549/DDP. The elucidation of mechanism and discovery of new potential targets may help us have a better understanding of cisplatin resistance.

2019-08-12 | PXD013265 | Pride

The marine diterpenes pseudopteroxazole (Ptx) and pseudopterosin G (PsG) target the integrity of the gram-positive cell wall

Project description:Pseudopteroxazole (Ptx) and the pseudopterosins are marine natural products with promising antibacterial potential. While Ptx has attracted interest for its anti-mycobacterial activity, pseudopterosins are active against several clinically relevant pathogens. Both compound classes exhibit low cytotoxicity and accessibility to targeted synthesis, yet their antibacterial mechanisms remain elusive. In this study, we investigated the modes of action of Ptx and pseudopterosin G (PsG) in Bacillus subtilis employing an unbiased approach that combines gel-based proteomics with a mathematical similarity analysis of response profiles. Proteomic responses to sublethal concentrations of Ptx and PsG were compared to a library of antibiotic stress response profiles revealing that both induce a stress response characteristic for agents targeting the bacterial cell envelope by interfering with membrane-bound steps of cell wall biosynthesis. Microscopy-based assays confirmed that both compounds compromise the integrity of the bacterial cell wall without disrupting the membrane potential.

2024-01-04 | PXD045994 | Pride

Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B

Project description:HDX-MS of R15B and it's interactions with trimeric eIF2 substrate. Here we integrated diverse approaches to elucidate how the PP1 non-catalytic subu-nit PPP1R15B (R15B) captures its full trimeric eIF2 substrate. We found that the substrate recruitment module of R15B is largely disordered with three short helical elements, H1, H2 and H3. H1 and H2 form a clamp that grasps the substrate in a re-gion remote from the phosphorylated residue. A homozygous N423D variant, adja-cent to H1, reducing substrate binding and dephosphorylation was discovered in a ra-re syndrome with microcephaly, development delay and intellectual disability. These findings explain how R15B captures its 125 kDa substrate by binding the far end of the complex relative to the phospho-site to present it for dephosphorylation by PP1, a paradigm of broad relevance.

2024-05-22 | PXD047538 | Pride

Ionophore 4-Br-A23187 causes copper stress in B. subtilis

Project description:Ionophores are small molecules or peptides that transport metal ions across biological membranes. Their transport capabilities are typically characterized in vitro using vesicles and single ion species. It is difficult to infer from these data which effects ionophores have on living cells in a complex environment (e.g. culture medium), since net transport is influenced e.g. by ion composition, concentration gradients, pH gradient, and active transport. To gain insights into the antibacterial mechanism of the semi-synthetic polyether ionophore 4-Br-A23187, we investigated its effects on the gram-positive model organism Bacillus subtilis. Changes in intracellular ion concentrations were determined using ionomics and the physiological impact was assessed by proteomics. 4-Br-A23187 treatment resulted in an increase in intracellular copper levels, an effect that was dependent on the copper concentration of the medium. The antibiotic effect of 4-Br-A23187 is further aggravated by a decrease in intracellular manganese and magnesium. Effects of copper hyperaccumulation, mirrored by the proteomic response, included oxidative stress, disturbance of proteostasis, metal, and sulfur homeostasis. Especially solvent-exposed iron-sulfur clusters like that of aconitase of the citric acid cycle are readily destabilized by copper. Using calcein fluorescence quenching as a readout, we confirmed in vitro that 4-Br-A23187 acts as copper ionophore.

2022-06-08 | PXD028938 | Pride