Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - American Gut Project - Subset of High vs Low Plant Eaters - MZmine Processing for FBMN

ABSTRACT: This desposit contains the MZmine project and files for Feature-Based Molecular Networking analysis after MZmine processing. The data are for plant eaters who consume more than 30 types of plants vs. those who do not. See the MSV000080186 at https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=6ab8eb3e05fb47dcac3b3bab03f00e67 [doi:10.25345/C5W946]

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Pieter Dorrestein

PROVIDER: MSV000084095 | GNPS | Mon Jul 15 15:29:00 BST 2019

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - IIN - Urine biomarker discovery

Project description:Diluted urine for biomarker discovery. Processed in MZmine 2.37.corr17.7_kei_merge2 GNPS link for IIN paper: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a5480529261b4a13bb867f2edad1dcbe

2019-07-29 | MSV000084148 | GNPS

GNPS - Bioactive molecular networking for sulfonolipids - MZmine Processing for FBMN

Project description:This dataset contains the raw data used for MZmine processing and Feature-based molecular networking of semi-purified fractions obtained from A. timonensis used for bioactive molecular networking to reveal contribution of sulfonolipids to observed biological activity.

2023-05-08 | MSV000091884 | GNPS

MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.

Project description:BackgroundMass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2.ResultsA key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms.ConclusionsMZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.

| S-EPMC2918584 | biostudies-literature

Teredinibacter sp. 2052S Quorum Sensing Untargeted Metabolomics

Project description:Raw LC-MS/MS data of crude extract of Teredinibacter sp. 2052S quorum sensing regulon https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=23f7062e523f49b18e13e4ca13715cfa

2021-12-23 | MSV000088613 | MassIVE

GNPS Optimisation SPE Oasis HLB Prime - EMP500 fecal sample

Project description:GNPS Optimisation SPE Oasis HLB Prime (Hydrophilic-Lipophilic-Balance, 30 mg with particle sizes of 30 um) using an EMP500 fecal sample. LC-MS/MS analysis of the different washing/elution steps on the Q-Exactive, using a C18 polar column. https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=2d2bb49239834407a5f1a8b0defad6e3 https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=3741451758824952886f765c9990a52b

2019-02-03 | MSV000083395 | GNPS

Lesion Detection Assessment in the Liver: Standard vs Low Radiation Dose Using Varied Post-Processing Techniques

Project description:To compare 2 different image creation/processing techniques during a standard CT scan in order to "see" problems in the liver and learn which method provides better image quality. The techniques use new artificial intelligence software to decrease image noise, which helps the radiologist to evaluate.

| 2244256 | ecrin-mdr-crc

A strategy for rapid discovery of traceable chemical markers in herbal products using MZmine 2 data processing toolbox: A case of Jing Liqueur.

Project description:ObjectiveThe quality evaluation of herbal products remains a big challenge. Traceable markers are the core concept of the authentication of herbal products. However, the discovery of traceable markers is labor-intensive and time-consuming. The aim of this study is to develop a convenient approach to rapidly screen the traceable markers for herbal product authentication.MethodsCommercial Jing Liqueur and its 22 species of herbal ingredients were analyzed using HPLC-QTOF-MS and GC-MS to characterize nonvolatile and volatile chemicals. The acquired data were imported into MZmine 2 software for mass detection, chromatogram building, deconvolution and alignment. The aligned data were exported into a csv file and then traceable markers were selected using the built-in filter function in Excel. Finally, the traceable markers were identified by searching against online databases or publications, some of which were confirmed by reference standards.ResultsA total of 288 chemical features transferred from herbal materials to Jing Liqueur product were rapidly screened out. Among them, 52 markers detected by HPLC-QTOF-MS were annotated, while nine volatile markers detected by GC-MS were annotated. Moreover, 30 of these markers were confirmed by comparing with reference standards. A chemical fingerprint consisting of traceable markers was finally generated to ensure the authentication and quality consistency of Jing Liqueur.ConclusionA strategy for rapid discovery of traceable markers in herbal products using MZmine 2 software was developed.

| S-EPMC9476759 | biostudies-literature

GNPS Teredinibacter sp. 2052S Quorum Sensing Untargeted Metabolomics

Project description:Raw LC-MS/MS data of crude extract of Teredinibacter sp. 2052S quorum sensing regulon https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=23f7062e523f49b18e13e4ca13715cfa

2021-12-23 | MSV000088613 | GNPS

GNPS - IIN - Stachybotrys metabolites

Project description:Stachybotrys, natural product discovery study, extracts, filtrates, mycelium, wildtype, overexpression, Stachybotrysins, Stachybonoids, Stachybotrydials For ion identity networking paper. GNPS link: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=0308d797c31a477292fe009030d03da7

2019-07-25 | MSV000084134 | GNPS

NF90 modulates processing of a subset of human pri-miRNAs.

Project description:MicroRNAs (miRNAs) are predicted to regulate the expression of >60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The double stranded RNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of primary miRNAs (pri-miRNAs). Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA electrophoretic mobility shift assay (EMSA). NF90-bound and downregulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly reduced. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.

| S-EPMC7337520 | biostudies-literature

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