Holo omic investigation of host and microbe in broiler chicken (HoloFood Trial 1/2/3)
Ontology highlight
ABSTRACT: Chicken farming is critical for future food security, yet there is still a need for improving animal welfare and optimised feeding strategies. HoloFood will explore the interaction and impact of the microbiome together with the host (animal) in response to different feeding strategies already implemented commercially. Chicken farming has recently made huge efforts towards healthy, natural food production without using chemicals or antibiotics in food systems. As such natural alternatives, such as prebiotic and probiotic additives to chicken feed, have been a huge improvement. Nonetheless, the full impact of these natural alternatives and the variation in chicken growth is still poorly understood. HoloFood aims to investigate the effect and interplay between the host (chicken) - microbiome in response to different dietary additives. HoloFood Trial 1/2/3 is reported in the current study MTBLS6988. HoloFood Trial A - seaweed-dose response is reported in MTBLS4381. HoloFood Trial B - blue mussel-dose response is reported in MTBLS4382. HoloFood Trial C - blue mussel ensilage-dose response is reported in MTBLS4384. HoloFood Trial D - fermented seaweed open water-dose response is reported in MTBLS6733. Linked cross omic data sets: Nucleic acid data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB43192. Metagenomic data associated with this study are available from MGnify under the Super Study 'holofood'.
INSTRUMENT(S): Liquid Chromatography MS - positive - reverse phase
SUBMITTER: Jacob Rasmussen Varsha Kale Sandy Rogers
PROVIDER: MTBLS6988 | MetaboLights | 2023-06-13
REPOSITORIES: MetaboLights
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2023-06-13 | MTBLS4381 | MetaboLights
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2023-06-13 | MTBLS4384 | MetaboLights
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2020-07-14 | MSV000085747 | GNPS
Project description:<p>Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.</p><p><br></p><p>In MTBLS1333, 58 lipid mediator standards were used to study the lipid fragmentation, build optimal collision energy models, create in-silico spectral libraries and spike-in as internal standards. They were purchased from Cayman Chemical (Ann Arbor, Michigan, USA). Lipid fragment masses of mediators were validated with the Metlin database (https://metlin.scripps.edu/).</p><p><br></p><p>Studies linked to this manuscript include;</p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1333' rel='noopener noreferrer' target='_blank'>MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1334' rel='noopener noreferrer' target='_blank'>MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1369' rel='noopener noreferrer' target='_blank'>MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1375' rel='noopener noreferrer' target='_blank'>MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1376' rel='noopener noreferrer' target='_blank'>MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1381' rel='noopener noreferrer' target='_blank'>MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/mtbls1382' rel='noopener noreferrer' target='_blank'>MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation</a></p>
2020-07-16 | MSV000085765 | GNPS
Project description:<p>Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.</p><p><br></p><p>In MTBLS1382, to validate lipid mediator species identified with the Qtrap instrument (<a href='https://www.ebi.ac.uk/metabolights/MTBLS1381' rel='noopener noreferrer' target='_blank'>https://www.ebi.ac.uk/metabolights/MTBLS1381</a>), the Thermo QEx HF was used to perform high resolution MS full scan (HR-FS) and data independent acquisition (DIA) analyses between 200-400 m/z with a 20 m/z step size. DIA method preparation and data analysis were performed with Skyline. We used LipidCreator as an external tool in Skyline to generate a collision-energy specific transition list for the mediators 12-HETE, 13-HODE, 15-HETE, arachidonic acid (AA),<strong> </strong>docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and thromboxane B2 (TXB2) and their deuterated counterparts 12-HETE-d8, 13-HODE-d4, 15-HETE-d8, AA-d8, DHA-d5, EPA-d5 and TXB2-d4, at a normalized collision energy NCE=21. We also used LipidCreator's relative fragment intensity prediction model to generate a custom spectral library for the light and heavy mediators. We transfered both the transition list and the spectral library directly from LipidCreator to Skyline and exported the dot product values after manual fragment peaks review.</p><p><br></p><p>Studies linked to this manuscript include;</p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1333' rel='noopener noreferrer' target='_blank'>MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1334' rel='noopener noreferrer' target='_blank'>MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1369' rel='noopener noreferrer' target='_blank'>MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1375' rel='noopener noreferrer' target='_blank'>MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1376' rel='noopener noreferrer' target='_blank'>MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1381' rel='noopener noreferrer' target='_blank'>MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1382' rel='noopener noreferrer' target='_blank'>MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation</a></p>
2020-06-26 | MSV000085632 | GNPS
Project description:<p>Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.</p><p><br></p><p>In MTBLS1381, to validate the performance and accuracy of the transition lists provided by LipidCreator and their applicabability on other MS platforms, we used the transition lists for targeted profiling of lipid mediators in human platelet material. Platelets were stimulated with 0.01 U/ml thrombin, 1 U/ml thrombin, 1 µg/ml CRP or 5 µg/ml CRP for 5 min. The MS profiling of unstimulated and stimulated platelet material (pellet and supernatant) was performed after HPLC separation on an AB Sciex QTrap 6500 (Applied Biosystems, Darmstadt, Germany) in negative mode. Samples were measured in triplicates, interspersed with blank and standard runs.</p><p><br></p><p>Studies linked to this manuscript include;</p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1333' rel='noopener noreferrer' target='_blank'>MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1334' rel='noopener noreferrer' target='_blank'>MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1369' rel='noopener noreferrer' target='_blank'>MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1375' rel='noopener noreferrer' target='_blank'>MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1376' rel='noopener noreferrer' target='_blank'>MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1381' rel='noopener noreferrer' target='_blank'>MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1382' rel='noopener noreferrer' target='_blank'>MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation</a></p>
2020-07-14 | MSV000085743 | GNPS
Project description:<p>Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.</p><p><br></p><p>In MTBLS1376, to validate the performance and accuracy of the transition lists provided by LipidCreator, we validated our theoretical calculations and the transition lists computed by LipidCreator experimentally, monitoring true and false targets on the model organism Saccharomyces <em>cerevisiae</em>. The lipidome of the yeast S. <em>cerevisiae</em> is well described and has been thoroughly investigated before. It has a limited number of fatty acyls and double bonds, and certain fatty acyls and lipid classes do not occur in it, which is important for our consecutive false identification calculations. Therefore, the yeast matrix from the theoretical calculation, 21 target lipids and 21 decoy lipids from commercially available lipid standards that are known to not be present in the yeast lipidome were selected. Based on our previous results, none of the lipid species was redundant among all three sets.</p><p><br></p><p>Studies linked to this manuscript include;</p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1333' rel='noopener noreferrer' target='_blank'>MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HF</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1334' rel='noopener noreferrer' target='_blank'>MTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTof</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1369' rel='noopener noreferrer' target='_blank'>MTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1375' rel='noopener noreferrer' target='_blank'>MTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1376' rel='noopener noreferrer' target='_blank'>MTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identification</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1381' rel='noopener noreferrer' target='_blank'>MTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator Profiling</a></p><p><a href='https://www.ebi.ac.uk/metabolights/MTBLS1382' rel='noopener noreferrer' target='_blank'>MTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation</a></p>
2020-07-31 | MSV000085865 | GNPS
Project description:<p>Hepatic fibrosis decreased feces bile acid level. Hepatic fibrosis increased serum bile acid. This result showed that hepatic fibrosis inhibited the excretion of bile acid in clinical patients. This result provided phenotype for hepatic fibrosis patients. Bile acid was important indexes for liver injury. TCDCA was important, and it play toxicity effect through ferroptosis and apoptosis. The research for other bile acid such CA, UDCA, TUDCA, TDCA, LCA, TLCA would be important.</p><p><br></p><p><strong>Hepatic fibrosis serum (sample 1) analysis</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS6732' rel='noopener noreferrer' target='_blank'><strong>MTBLS6732</strong></a>.</p><p><strong>Hepatic fibrosis feces (sample 2) analysis</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS6742' rel='noopener noreferrer' target='_blank'><strong>MTBLS6742</strong></a>.</p><p><strong>Hepatic fibrosis serum+feces (sample 3) analysis</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS6728' rel='noopener noreferrer' target='_blank'><strong>MTBLS6728</strong></a>.</p>
2023-03-17 | MTBLS6732 | MetaboLights