Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS Incorporating LC-MS/MS Analysis and the Dereplication of Natural Product Samples into an Upper-Division Undergraduate Laboratory Course

ABSTRACT: This dataset represents a collection of chromatography fractions derived from botanical extractions. These chromatography fractions were chosen based upon demonstrated antioxidant activity following a standard DPPH assay. Echinacea-1 is the E. angustifolia sample while -2 and -3 were identified as E. purpurea. All collected samples have voucher specimens held in the URI Herbarium.

INSTRUMENT(S): LTQ

ORGANISM(S): Hypericum Perforatum (ncbitaxon:65561) Berberis Thunbergii (ncbitaxon:121720) Sambucus Nigra (ncbitaxon:4202) Actaea Racemosa (ncbitaxon:64040) Echinacea Angustifolia (ncbitaxon:308558) Echinacea Purpurea (ncbitaxon:53751) Humulus Lupulus (ncbitaxon:3486) Salvia Rosmarinus (ncbitaxon:39367) Withania Somnifera (ncbitaxon:126910) Aloe Vera (ncbitaxon:34199)

SUBMITTER: Matt Bertin

PROVIDER: MSV000088444 | GNPS | Wed Nov 24 12:44:00 GMT 2021

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Incorporating LC-MS/MS Analysis and the Dereplication of Natural Product Samples into an Upper-Division Undergraduate Laboratory Course

Project description:This dataset represents a collection of chromatography fractions derived from botanical extractions. These chromatography fractions were chosen based upon demonstrated antioxidant activity following a standard DPPH assay. Echinacea-1 is the E. angustifolia sample while -2 and -3 were identified as E. purpurea. All collected samples have voucher specimens held in the URI Herbarium.

2021-11-24 | MSV000088444 | MassIVE

UPLC-MS-ELSD-PDA as a powerful dereplication tool to facilitate compound identification from small-molecule natural product libraries.

Project description:The generation of natural product libraries containing column fractions, each with only a few small molecules, using a high-throughput, automated fractionation system, has made it possible to implement an improved dereplication strategy for selection and prioritization of leads in a natural product discovery program. Analysis of databased UPLC-MS-ELSD-PDA information of three leads from a biological screen employing the ependymoma cell line EphB2-EPD generated details on the possible structures of active compounds present. The procedure allows the rapid identification of known compounds and guides the isolation of unknown compounds of interest. Three previously known flavanone-type compounds, homoeriodictyol (1), hesperetin (2), and sterubin (3), were identified in a selected fraction derived from the leaves of Eriodictyon angustifolium. The lignan compound deoxypodophyllotoxin (8) was confirmed to be an active constituent in two lead fractions derived from the bark and leaves of Thuja occidentalis. In addition, two new but inactive labdane-type diterpenoids with an uncommon triol side chain were also identified as coexisting with deoxypodophyllotoxin in a lead fraction from the bark of T. occidentalis. Both diterpenoids were isolated in acetylated form, and their structures were determined as 14S,15-diacetoxy-13R-hydroxylabd-8(17)-en-19-oic acid (9) and 14R,15-diacetoxy-13S-hydroxylabd-8(17)-en-19-oic acid (10), respectively, by spectroscopic data interpretation and X-ray crystallography. This work demonstrates that a UPLC-MS-ELSD-PDA database produced during fractionation may be used as a powerful dereplication tool to facilitate compound identification from chromatographically tractable small-molecule natural product libraries.

| S-EPMC4784093 | biostudies-literature

Dereplication of Lantana trifolia L. leaves and fruits by UFLC-DAD-ESI (+)-MS/MS

Project description:Thsi is a study of anti-Candida activities of the fractions obtained from the fruits and leaves of two Lantana trifolia specimens collected in different sites of Minas Gerais State in Brazil

2023-04-19 | MSV000091744 | MassIVE

High-resolution MS, MS/MS, and UV database of fungal secondary metabolites as a dereplication protocol for bioactive natural products.

Project description:A major problem in the discovery of new biologically active compounds from natural products is the reisolation of known compounds. Such reisolations waste time and resources, distracting chemists from more promising leads. To address this problem, dereplication strategies are needed that enable crude extracts to be screened for the presence of known compounds before isolation efforts are initiated. In a project to identify anticancer drug leads from filamentous fungi, a significant dereplication challenge arises, as the taxonomy of the source materials is rarely known, and, thus, the literature cannot be probed to identify likely known compounds. An ultraperformance liquid chromatography-photodiode array-high-resolution tandem mass spectrometric (UPLC-PDA-HRMS-MS/MS) method was developed for dereplication of fungal secondary metabolites in crude culture extracts. A database was constructed by recording HRMS and MS/MS spectra of fungal metabolites, utilizing both positive- and negative-ionization modes. Additional details, such as UV-absorption maxima and retention times, were also recorded. Small-scale cultures that showed cytotoxic activities were dereplicated before engaging in the scale-up or purification processes. Using these methods, approximately 50% of the cytotoxic extracts could be eliminated from further study after the confident identification of known compounds. The specific attributes of this dereplication methodology include a focus on bioactive secondary metabolites from fungi, the use of a 10 min chromatographic method, and the inclusion of both HRMS and MS/MS data.

| S-EPMC3856222 | biostudies-literature

Opisthorchis felineus excretory-secretory product (ESP) and lysate proteomics by GeLC-MS / MS

Project description:A significant number of pathological conditions, accompanied by chronic non-healing wounds, demands searching for new modern therapeutic approaches. Well-documented ability of O. felineus to initiate extracellular matrix (ECM) remodeling and liver epithelium regeneration suggests that its bioactive molecules may stimulate skin wound healing processes. The aim of this study was to investigate the wound healing potential of the Opisthorchis felineus excretory-secretory and lysate proteins on a murine model. The following methods were used for the study: histological (wounded skin condition), immunohistochemical (ECM, neoangiogenesis, O. felineus GST and TPx proteins), gene expression analysis (inflammation, angiogenesis, ECM condition). O. felineus excretory-secretory product (ESP) and lysate proteins have revealed wound-healing potential, they: i) reduce inflammation levels, ii) modulate vascular response, iii) stimulate collagen deposition and dermal ECM remodeling. Additional proteomic analysis of adult O. felineus ESP and lysate samples was conducted. Proteomic analysis approach called GeLC-MS / MS was chosen to study of the excretory-secretory product and lysate proteins. This approach is based on one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), in-gel protein digestion with trypsin followed by liquid chromatography-tandem mass spectrometry. The SDS-PAGE step allow to removes hemozoin also as detergents, buffers and salts from the protein extract that may interfere with mass spectrometry analysis

2023-03-11 | PXD037991 | Pride

Transcriptomic responses of caddisfly Dicosmoecus gilvipes to temperature.

Project description:These samples are from RNA collected from specimens held at 4 temperatures (15.5, 20.0, 25.0 and 28.6degC). Specimens were ramped to one of those temperatures over 4 days following a common garden at 11degC for two weeks. RNA was extracted from thorax tissue and used for RNA-seq. Genes with statistically different expression levels among temperatures were identified.

2022-06-20 | GSE206349 | GEO

UHPLC-ESI-QTOF-MS/MS-Based Molecular Networking Guided Isolation and Dereplication of Antibacterial and Antifungal Constituents of Ventilago denticulata.

Project description:Ventilago denticulata is an herbal medicine for the treatment of wound infection; therefore this plant may rich in antibacterial agents. UHPLC-ESI-QTOF-MS/MS-Based molecular networking guided isolation and dereplication led to the identification of antibacterial and antifungal agents in V. denticulata. Nine antimicrobial agents in V. denticulata were isolated and characterized; they are divided into four groups including (I) flavonoid glycosides, rhamnazin 3-rhamninoside (7), catharticin or rhamnocitrin 3-rhamninoside (8), xanthorhamnin B or rhamnetin 3-rhamninoside (9), kaempferol 3-rhamninoside (10) and flavovilloside or quercetin 3-rhamninoside (11), (II) benzisochromanquinone, ventilatones B (12) and A (15), (III) a naphthopyrone ventilatone C (16) and (IV) a triterpene lupeol (13). Among the isolated compounds, ventilatone C (16) was a new compound. Moreover, kaempferol, chrysoeriol, isopimpinellin, rhamnetin, luteolin, emodin, rhamnocitrin, ventilagodenin A, rhamnazin and mukurozidiol, were tentatively identified as antimicrobial compounds in extracts of V. denticulata by a dereplication method. MS fragmentation of rhamnose-containing compounds gave an oxonium ion, C6H9O3+ at m/z 129, while that of galactose-containing glycosides provided the fragment ion at m/z 163 of C6H11O5+. These fragment ions may be used to confirm the presence of rhamnose or galactose in mass spectrometry-based analysis of natural glycosides or oligosaccharide attached to biomolecules, that is, glycoproteins.

| S-EPMC7558283 | biostudies-literature

A high-throughput method for dereplication and assessment of metabolite distribution in <i>Salvia</i> species using LC-MS/MS.

Project description:Dereplication of crude plant extracts through liquid chromatography-mass spectrometry is a powerful technique for the discovery of novel natural products. Unfortunately, this technique is often plagued by a low level of confidence in natural product identification. This is mainly due to the lack of extensive chromatographic and mass spectrometric optimizations that result in improper and incomplete MS/MS fragmentation data. This study proposes a solution to this problem by the optimization of chromatographic separation and mass spectrometry parameters. We report herein a direct and high-throughput strategy for natural product dereplication in five Salvia species using high-resolution ESI-QTOF-MS/MS data. In the present study, we were able to identify a total of forty-seven natural products in crude extracts of five Salvia species using MS/MS fragmentation data. In addition to dereplication of Salvia species, quantitative profiling of twenty-one bioactive constituents of the genus was also performed on an ion trap mass spectrometer. For the quantitation study, method development focused on chromatographic optimizations to achieve maximum sensitivity. The developed dereplication and quantitation strategy can be extended to develop comprehensive metabolic profiles of other plant genera and species and thus can prove useful in the field of drug discovery from plants.

| S-EPMC7082496 | biostudies-literature

LC-PDA-MS/MS-Based Dereplication Guided Isolation of a New Optical Isomer of 19,20-Epoxycytochalasin-N and Its Cytotoxic Activity.

Project description:The Rosellinia sanctae-cruciana extract was subjected to detailed liquid chromatography tandem mass spectrometry studies. A total of 38 peaks were annotated to m/z 508.26, m/z 510.28, m/z 524.26, m/z 526.28, m/z 540.26, m/z 542.27, and m/z 584.28 [M + H]+. The accurate mass, mutually supported UV/vis spectra, and database search identified these compounds as cytochalasins. Systematic dereplication helped identify a peak at m/z 540.26 [M + H]+ as the new compound. Further, the identified compound was purified by high-performance liquid chromatography and characterized by 2D NMR to be 19,20-epoxycytochalasin N1, a new optical isomer of 19,20-epoxycytochalasin-N. It exhibited substantial cytotoxicity with IC50 values ranging from 1.34 to 19.02 μM. This study shows a fast approach for dereplicating and identifying novel cytochalasin metabolites in crude extracts.

| S-EPMC9404496 | biostudies-literature

2af0d6d0-7214-440c-a3ff-7189eefec97a - samples

Project description:Plasma from lung cancer patients from EDTA tubes was fractionated using size exclusion chromatography. Fractions 1-5, 7-11, 12-15, 16-20 were pooled, cfDNA was extracted from the fractions and paired unfractionated samples and PE150bp sequencing was performed on an Illumina Novaseq S4 flowcell. Samples are provided as raw reads without any prior processing.

| EGAD00001009780 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data