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GNPS - Molecular networking as a dereplication strategy -Figure 4

ABSTRACT: Molecular networking as a dereplication strategy. Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. J Nat Prod. 2013 Sep 27;76(9):1686-99. doi: 10.1021/np400413s PubMedID: 24025162 RAW Files used to generate Figure 4. Bacterial network with a cosine similarity score cutoff of 0.65. This network was generated from direct infusion of extracts or direct nanoDESI-MS/MS sampling of eight bacteria, 14 known compounds

INSTRUMENT(S): LTQ FT

ORGANISM(S): Data From Multiple Bacteria

SUBMITTER: Dorrestein and Gerwick

PROVIDER: MSV000078547 | GNPS | Tue Feb 11 14:08:00 GMT 2014

REPOSITORIES: GNPS

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Publications

Molecular networking as a dereplication strategy.

Yang Jane Y JY Sanchez Laura M LM Rath Christopher M CM Liu Xueting X Boudreau Paul D PD Bruns Nicole N Glukhov Evgenia E Wodtke Anne A de Felicio Rafael R Fenner Amanda A Wong Weng Ruh WR Linington Roger G RG Zhang Lixin L Debonsi Hosana M HM Gerwick William H WH Dorrestein Pieter C PC

Journal of natural products 20130911 9

A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized or ...[more]

PMID: 24025162

Similar Datasets

GNPS - Molecular networking as a dereplication strategy-Figure 3

Project description:Molecular networking as a dereplication strategy. Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. J Nat Prod. 2013 Sep 27;76(9):1686-99. doi: 10.1021/np400413s PubMedID: 24025162 RAW Files used to generate Figure 3. Cyanobacterial network with a cosine similarity score cutoff of 0.65. This network was generated when extracts of cyanobacteria (six distinct collections) were separated into nine fractions based on polarity and then analyzed via LC-MS/MS with five known compounds

2014-02-11 | MSV000078548 | GNPS

Smooth muscle cell mineralocorticoid receptor regulation of vascular mRNAs with aging

Project description:We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic mRNA to examine the effect of age on vascular mRNA alterations in the presence and absence of SMC-MR. For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

2017-08-10 | GSE102397 | GEO

Smooth muscle cell mineralocorticoid receptor regulation of vascular microRNAs with aging

Project description:We used a smooth muscle cell-specific mineralocorticoid receptor knockout mouse to generate young and aged MR-intact and SMC-MR-KO aortic miRNA to examine the effect of age on vascular miRNA alterations in the presence and absence of SMC-MR. For more information about the mouse model see: McCurley, A et al. Direct regulation of blood pressure by smooth muscle cell mineralocorticoid receptors. Nat Med. 2012 Sep;18(9):1429-33

2016-07-29 | GSE84960 | GEO

Molecular networking as a dereplication strategy.

Project description:A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.

| S-EPMC3936340 | biostudies-literature

Smooth muscle cell mineralocorticoid receptor regulation of vascular microRNAs with aging

2016-07-29 | E-GEOD-84960 | biostudies-arrayexpress

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Project description:Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.

| S-EPMC6786971 | biostudies-literature

Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data

Project description:This SuperSeries is composed of the SubSeries listed below. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. RekinM-bM-^@M-^Ys Janky, Annelien Verfaillie, Hana ImrichovM-CM-!, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, and Stein Aerts. PLOS Computational Biology, 2014. Refer to individual Series

2014-05-27 | E-GEOD-47043 | biostudies-arrayexpress

Perilous Sites: High basic Fibroblast Growth Factor level supplement Parkinson’s disease pathology and its Spread

Project description:Lewy body (LB) pathology and loss of dopaminergic neurons are imprints of Parkinson’s disease (PD). LBs are mainly comprised of alpha-Synuclein (Dijkstra et al., 2014). Strolling detection of LBs in brain regions contribute to progressive construct of PD pathology to which molecular mechanisms are not clear (H. Braak & Del Tredici, 2017). Two key facets of LB formation are protein aggregation via misfolding and transmission of misfoldled proteins to various brain regions, eventually causing neuronal death (Goedert, Spillantini, Del Tredici, & Braak, 2013; Pacelli et al., 2015). Misfolding requires alterations in intracellular physiology (Carbone, Costa, Provensi, Mannaioni, & Masi, 2017; Funes et al., 2014; Guzman et al., 2018; Pacelli et al., 2015) and detection of misfolded proteins in exosomes confirms exosomatic transmission (Ngolab et al., 2017). High levels of neurotropic-factors (Brockmann et al., 2017) and changes in bioenergetics are found in PD patients, these can bring physiological alterations (Smith et al., 2018). En masse, these evidences and hipocampal association with synucleopathies (Flores-Cuadrado, Ubeda-Bañon, Saiz-Sanchez, de la Rosa-Prieto, & Martinez-Marcos, 2016) allowed us to probe other volunerable PD proteins in cell-lysate and exosomal proteomes of bFGF treated hippocampal neurons. Using WPCNA we developed co-expression modules and spotted many PD related proteins; which can act as precursors during diseased or onset stage.

2020-07-21 | PXD015969 | Pride

The Global Landscape of Multiscale Transcriptomic Networks and Key Regulators in Parkinson’s Disease

Project description:Despite the advance of genetic and genomic analysis of Parkinson’s disease (PD), our understanding of PD pathophysiology remains limited due to unclear etiology of idiopathic PD and unavailable integrated approach for large-scale multi-dimensional data. Herein we report a novel multiscale network approach to establish transcriptomic network from postmortem PD brain data. The analysis delineates structures of gene-gene regulatory networks in PD and identifies novel network regulators that are functionally connected to previously identified PD risk genes. We identify STMN2, encoding a neuron-specific stathmin family protein and down-regulated in PD brains, as the top regulator of the transcriptomic network underlying PD. Knock-down of Stmn2 in mice validates its regulatory role, and Stmn2 deficient mice show dopaminergic neuron vulnerability, phosphorylated a-synuclein elevation, and locomotor function deficits. As predicted from the network analysis, reduced STMN2 expression impairs synaptic vesicle trafficking in midbrain neurons. Our approach sheds light on the complexity of PD pathogenic network and thus facilitates identification of novel PD therapeutic targets.

2019-12-03 | GSE114840 | GEO

An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures.

Project description:A fundamental factor in natural product drug discovery programs is the necessity to identify the active component(s) from complex chemical mixtures. Whereas this has traditionally been accomplished using bioassay-guided fractionation, we questioned whether alternative techniques could supplement and, in some cases, even supplant this approach. We speculated that a combination of ligand-fishing methods and modern analytical tools (e.g., LC-MS and online natural product databases) offered a route to enhance natural product drug discovery. Herein, a candidate solution referred to as the lickety-split ligand-affinity-based molecular angling system (LLAMAS) is described. This approach utilizes an ultrafiltration-based LC-PDA-MS/MS-guided DNA-binding assay in combination with the (i) Global Natural Products Social Molecular Networking, (ii) Dictionary of Natural Products, and (iii) SciFinder platforms to identify DNA binders in complex chemical mixtures. LLAMAS was initially vetted in tests using known small-molecule DNA binders and then optimized to a 96-well plate-based format. A set of 332 plant samples used in traditional Chinese medicine was screened for DNA-binding activity with LLAMAS, resulting in the identification of seven DNA-binding molecules, including berberine (12), palmatine (13), coptisine (14), fangchinoline (15), tetrandrine (16), daurisoline (17), and dauricine (18). These results demonstrate that LLAMAS is an effective natural product discovery platform for the efficient identification and dereplication of DNA-binding molecules from complex mixtures.

| S-EPMC9229839 | biostudies-literature

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