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10 results for “metabolite annotation”
Software and suspect database for: "A large scale multi-laboratory suspect screening of pesticide metabolites in human biomonitoring: From tentative annotations to verified occurrences"
<p>This upload contains the pesticide suspect list aggregated among the laboratories of work package 16 of the HBM4EU (https://www.hbm4eu.eu) project for a large-scale pesticide suspect screening and the resolving search templates for each pesticide. Additionally, we provide the used software version of MetAlign applied in this screening.</p>
HSDB Metabolism / Metabolites Annotation Content from PubChem
<p>An archived version of annotation content extracted from PubChem for the <a href="https://pubchem.ncbi.nlm.nih.gov/source/11933">HSDB</a> section, as scripted up in <a href="https://gitlab.lcsb.uni.lu/eci/pubchem/-/blob/master/annotations/tps/extractAnnotations.R">extractAnnotations.R</a> (code available on the ECI <a href="https://gitlab.lcsb.uni.lu/eci/pubchem/">pubchem</a> repository)</p>
Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web
<p>This is the data and analysis scripts needed to recreate the analyses shown in "Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web"</p> <p>The abstract of the manuscript summarizes the goal of the paper:</p> <p> </p> <p>Stable isotope tracing is a crucial technique for understanding the metabolic wiring of biological systems, determining metabolic flux through pathways of interest, and detecting novel metabolites and pathways. Despite the potential insights provided by this technique, its application remains limited to a small number of targeted molecules and pathways. Because previous software tools usually require chemical formulas to find relevant features, and the data are highly complex, especially in untargeted metabolomics and when the reactions and metabolites downstream the labeled substrates are poorly characterized. We report here Khipu version 2 and its new user-friendly web application. New functions are added to enhance analyzing stable isotope tracing data including metrics that evaluate peak enrichment in labeled samples, scoring methods to facilitate robust detection of intensity patterns and integrated natural abundance correction. We demonstrate that this approach can be applied to untargeted metabolomics to systematically extract isotope-labeled compounds and annotate the unidentified metabolites.</p> <p> </p> <p>This repository stores the code and data needed to recreate all presented analyses. The code and instructions are in the AnalysisCode.zip. The DDA in the dda_mzML.zip, the MS1 in the dataset_mzml.zip, and the asari results in the AsariResults.zip. The readme is in the AnalysisCode.zip and has more detailed instructions. This directory also has the output data in tabular format for the figures as the figures were mostly made with Excel. </p>
Supplementary Data - Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer network
<p><strong>Supplementary data 1</strong>: Peak annotation evaluation between MetDNA1 and KGMN (MetDNA2)</p> <p><strong>Supplementary data 2</strong>: 46 standard mixture (46std_mix) and the knowledge-based metabolic reaction network</p> <p><strong>Supplementary data 3</strong>: KGMN results of 46std_mix data set and validation results</p> <p><strong>Supplementary data 4</strong>: KGMN results of NIST urine data sets and validation results</p> <p><strong>Supplementary data 5</strong>: KGMN results of different biological samples</p> <p><strong>Supplementary data 6</strong>: Recurrent unknowns of NIST urine via repository-mining</p> <p><strong>Supplementary data 7</strong>: Table of adducts, neutral losses, empirical rules in KGMN</p>
Fig. 5 in Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations
Fig. 5. Comparison of the experimental ECD spectra of 2 and calculated ECD spectra for stereoisomer of 2 shown in Fig. 2.
Fig. 1. Overall molecular network obtained from MZmine2 in Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations
Fig. 1. Overall molecular network obtained from MZmine2-preprocessed HPLC-MS2 data of C. scillifolium bulbs crude alkaloid extract and first chromatographic fractions. Triangle-shaped nodes are tentatively-tagged against ISDB and benefit from a taxonomical re-ranking of the tentative candidates (their structures are provided in Fig. S1, Supporting Information). Nodes highlighted in orange correspond to the targeted structures (1–4) in the phytochemical workflow. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations
Fig. 4. Comparison of the experimental ECD spectrum of 1 and calculated ECD spectrum for the (3S, 4aS, 10bS, 11S) enantiomer.
NMR and HRMS raw data for "Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking"
<p>Raw NMR data and HRMS data for synthesized compounds</p>
Fig. 2 in Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations
Fig. 2. Structures of compounds 1–4.
Fig. 3 in Streamlined targeting of Amaryllidaceae alkaloids from the bulbs of Crinum scillifolium using spectrometric and taxonomically-informed scoring metabolite annotations
Fig. 3. Key COSY and HMBC correlations of compounds 1–4.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.