Find research datasets worth reusing

opencc-zeroJul 2022View details →

LC-MS raw dataset of Dendrobium extracts

Orbitrap mass spectrometry is one kind of high-resolution mass analyzer containing multistage fragment monitoring, a selective fragmentation mode, and a personalized data acquisition method, which is widely applied in pharmacokinetic analysis, the food industry, environmental monitoring, and proteomics. Alkaloids are an important active ingredient in Dendrobium officinale, but there are few studies on their isolation and identification. Here, a combination method for separating and detecting alkaloids and their precursors was established. The accurate mass of the components separated by HPLC were determined using an high resolution mass analyzer. The multistage fragmentation pathway of alkaloids was speculated based on a database-dependent retrieval method. By using a SPE-HPLC-MS/MS method, the potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases.The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. Seven alkaloids were separated and identified from D. officinale, which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified.

openmit-licenseJul 2022View details →

Early Detection of Nucleation Events from Solution in LC-TEM by Machine Learning

These data are images taken with a liquid cell transmission electron microscope and annotation data of particles. See <a href="https://github.com/hiroyasukatsuno/Early-Detection-of-Nucleation-Events-LC-TEM">this page (GitHub)</a>.

opencc-by-4.0Oct 2022View details →

Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)

Proteomic Profiling Dataset for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)

opencc-by-4.0Nov 2017View details →

Proteomics LC-MS/MS test dataset for protein quantitation via stable isotope labelling

The provided mzML file can be used as a test dataset for protein identification and quantitation software. It was generated from human embryonic kidney (HEK) cells that were either unlabelled or labelled with heavy SILAC (K6R6, unimod accession 188, PSI-MS Name: "Label:13C(6)"). Apart from different labelling, the HEK cells were kept in exactly the same conditions and harvested simultaneously. Light and heavy labelled proteins from HEK cell lysate were mixed in a certain ratio, digested with Trypsin and measured on a ThermoFisher QExactive mass spectrometer. A more detailed description on the generation of the dataset will soon be accessible at PRIDE. The provided mzML file has been converted from Thermo RAW and slightly modified via msConvert (ProteoWizard). To reduce the filesize and to speed up analysis, it has further been filtered to contain only the data measured between 2,000 sec and 3,000 sec of the original LC-MS/MS run.

opencc-zeroApr 2024View details →

LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant

Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth muscle contraction. Specifically, the non-receptor kinase Src has been reported to phosphorylate Tyr198 and Tyr308 of mouse PANX1 (equivalent to Tyr199 and Tyr309 of human PANX1), resulting in channel opening and ATP release. Although the Src-dependent PANX1 activation mechanism has been widely discussed in the literature, independent validation of the tyrosine phosphorylation of PANX1 has been lacking. Here, we show that commercially available antibodies against the two phosphorylation sites mentioned above—which were used to identify endogenous PANX1 phosphorylation at these two sites—are nonspecific and should not be used to interpret results related to PANX1 phosphorylation. We further provide evidence that neither tyrosine residue is a major phosphorylation site for Src kinase in heterologous expression systems. We call on the field to re-examine the existing paradigm of tyrosine phosphorylation-dependent activation of the PANX1 channel.

opencc-by-3.0Sep 2021View details →

LC-QuAD 2.1

A cleaned dataset version of LC-QuAD 2.0 including: <ul> <li>Outliers and duplicated question removal</li> <li>Dummy SPARQL templates for Wikidata and DBpedia 2018</li> <li>Training/development/testing sets used on the paper  "A hereditary attentive template-based approach for Complex Knowledge Base Question Answering systems" <ul> <li>Two training sets: one with and without paraphrased questions </li> </ul> </li> </ul> The original dataset (LC-QuAD 2.0) can be found at http://lc-quad.sda.tech/

opencc-by-4.0Dec 2022View details →

Exploring the Effects of LC Parameters on Retention Indices of Small Molecules using Amine Scaling - Supplementary Data

In this document the retention times, calculated retention indices and calculated delta retention indices can be found that were used for the thesis on Exploring the Effects of LC Parameters on Retention Indices of Small Molecules using Amine Scaling, as well as the raw-data files of the performed measurements.

opencc-by-4.0Aug 2018View details →

LC-MS/MS data of pharmaceutical compounds for lIbrary building

Dataset used for MergeION package testing are provided by Janssen Pharmaceutica. It consists of known standard pharmaceutical compounds for which high quality Q-Exactive MS/MS data is provided. Details about these compounds can be found in Metadata_Library.txt. All datasets were acquired in positive ion mode through either DDA (data-dependent acquisition) or targeted MS/MS. Raw data in profile mode were converted into centroid-mode mzML or mzXML files using MSConvertGUI

openApr 2023View details →

LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-A"

LC-MS/MS data generated from plasma samples from children with bacterial and viral infections.

openApr 2023View details →

LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-B"

LC-MS/MS data generated from plasma samples from children with bacterial and viral infections.

opencc-by-4.0Aug 2023View details →

TBT exposure dataset of the manuscript "Assessment of endocrine disruptors effects on zebrafish (Danio rerio) embryos by untargeted LC-HRMS metabolomic analysis"

Raw LC-HRMS data of the TBT exposure of zebrafish embryos (for more details see https://doi.org/10.1016/j.scitotenv.2018.03.369) The exposure protocol involved zebrafish embryos exposed in groups of 20 to various concentrations of chemical compounds, with five replicates per treatment. The concentrations ranged from the lowest observed effect concentrations (LOECs) to control levels. After exposure, embryos were collected, washed, frozen, and stored. Metabolites were extracted from individual embryo pools using methanol and methionine sulfone. The extraction process included vortexing, sonication, and centrifugation, followed by addition of water and chloroform. The aqueous fraction was dried and reconstituted using acetonitrile-water solution. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was used for analysis. Chromatographic separations were carried out on a hydrophilic interaction liquid chromatography (HILIC) column. Mass spectrometry was performed using an Orbitrap mass spectrometer with electrospray ionization in positive and negative modes. The mass spectra were acquired at high resolution, and fragmentation scans were used for metabolite identification. The overall process aimed to analyze the metabolomic profile of zebrafish embryos exposed to different chemical concentrations. Data files <blockquote> TBT ESI+ (tbt_pos.rar) - CDF files - QC (4 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>   <blockquote> TBT ESI- (tbt_neg.rar) - CDF files - QC (6 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>

Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD) Extension Study for Subjects Previously Enrolled in Triheptanoin Studies

ClinicalTrials.gov study NCT02214160. IPD Sharing: Not stated. Countries: 2. Publications: 2.

Causal Relationships Between LC-omega-3-enriched Diet and Cognition

ClinicalTrials.gov study NCT01625195. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.

LC Bead Embolization Agent With Doxorubicin in the Treatment Liver Metastasis From Melanoma

ClinicalTrials.gov study NCT01010984. IPD Sharing: Not stated. Countries: 1. Publications: 2.

The LC Bead Trial; Transarterial Chemoembolization of Hepatocellular Carcinoma (HCC)With a Drug-eluting Bead

ClinicalTrials.gov study NCT01259024. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.

A Study of UX007 (Triheptanoin) in Participants With Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD)

ClinicalTrials.gov study NCT01886378. IPD Sharing: Not stated. Countries: 2. Publications: 4.

Efficacy and Safety of Immuncell-LC Group and Non-treatment Group in Hepatocelluar Carcinoma Patients

ClinicalTrials.gov study NCT00699816. IPD Sharing: Not stated. Countries: 1. Publications: 2.

publicApr 2024View details →

LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant

Open the record for dataset details and reuse information.