GNPS - Untargeted_Metabolomics_Tubingen_Summer_School_DOManalsis_Lab15
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Synechococcus (ncbitaxon:1129) Environmental Samples <bacillariophyta> (ncbitaxon:33858)
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000090181 | GNPS | Tue Aug 23 01:02:00 BST 2022
REPOSITORIES: GNPS
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Project description:LC-MSMS samples were acquired on QE HF from "Lab 15". Samples originate from marine dissolved organic matter and samples make up a dilution series.
2022-08-23 | MSV000090181 | MassIVE
Project description:<p>Particulate organic matter (fecal pellets) from zooplankton has been demonstrated to be important nutrient sources for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12-16 h of incubation. We measured bulk dissolved organic carbon, dissolved free amino acids via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16s rDNA amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.</p>
2020-11-27 | MTBLS1822 | MetaboLights
Project description:In this study, the efficiency of four RNA extraction methods was compared on 23 FFPE cardiac tissue specimens. The Qiagen AllPrep DNA/RNA FFPE kit (Method QP), Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization (Method QE), CELLDATA RNAstorm 2.0 FFPE RNA Extraction kit (Method BP) and CELLDATA RNAstorm 2.0 FFPE RNA Extraction Kit with protocol modifications on the lysis step (Method BL). In comparing RNA quality metrics across FFPE RNA extract, nucleic acids extracted with Method QE and QP had the highest RNA yield. However, Method QE outperformed Method QP as more extract from Method QE had DV 200 values above 30%. Both method BL and BP produced a similar range of RNA purity and yield but more extract from Method BL had DV 200 values above 30% compared to Method BP. When accessing distribution value, Method BL outperformed Methods BP, QE, and QP as more extracts from Method BL had DV 200 values above 30% (16/23 samples) compared to other methods (PDV200<0.001; Kruskal-Wallis). However, method QE outperformed other methods in terms of RNA yield. The sequencing performance of RNA extracts from Method QE and Method BL was further tested on 8 matching samples with high RNA yield and high DV200 value respectively. RNA extracts from Method QE which yielded the highest RNA quantity among all methods exhibited comparable sequencing performance to extract obtained through Method BL, which yielded extract with high DV200 value. This study suggests that the DV200 and RNA yield are both reliable pre-analytic metrics in determining a suitable method for successful transcriptome sequencing of FFPE samples and have important implications for future studies exploring transcriptome sequencing of FFPE cardiac specimens.
2024-05-23 | GSE267659 | GEO
Project description:Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism's proteome can therefore provide information on its interaction with the environment. Data dependen proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of isolated culture of bacteria (Ruegeria pomoeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
2017-02-01 | PXD004799 | Pride
Project description:Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism's proteome can therefore provide information on its interaction with the environment. Data dependen proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of isolated culture of bacteria (Ruegeria pomoeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
2017-02-02 | PXD004758 | Pride
Project description:Hela test samples prepared by FASP digestion were run on QE and QE-HF mass spectrometry as quality controls. We tried to compare the protein and peptide identification results between the two machines.
2022-09-18 | PXD028625 | JPOST Repository
Project description:Arabidopsis ecotype Col-0 expressing RPL18 fused to His & Flag epitopes (RPL18-HF) under 35S control was used to discern the effects of Turnip mosaic virus (TuMV) infection on host translation initiation. Plants were grown in LC-1 soil in 12 hour days and infected by TuMV-GFP or mock-inoculated just prior to sending up bolts. Samples were taken from rosette leaves 10 days after inoculation. Only tissue fluorescing GFP was selected from the virus-infected samples. Similar tissue was sampled from mock-infected leaves. FLAG antibody was used to isolate RPL18-HF. The RNA co-immunoprecipitated with RPL18-HF is fully translation-initiated. This translation-initiated RNA, also referred to as polysomal RNA, was isolated and compared to total RNA under both mock and TuMV-infected states to find TuMV-induced changes in host translation initiation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jackson Moeller. The equivalent experiment is AT42 at PLEXdb.]
2011-03-11 | GSE20278 | GEO
Project description:Low concentrations of the dissolved leonardite humic acid HuminFeed® (HF) prolonged the lifespan and enhanced the thermal stress resistance of the model organism Caenorhabditis elegans. Furthermore growth was impaired and reproduction delayed, effects which have also been identified in other polyphenolic monomers, including tannic acid, rosmarinic acid, and caffeic acid. Moreover, a chemical modification of HF (HF-HQ), which increases its phenolic/quinonoid moieties, magnified the biological impact on C. elegans. To gain a deep insight into the molecular basis of these effects, we performed global transcriptomics on young adult (3 d) and old adult (11 d) nematodes exposed to two concentrations of HF and young adults (3 d) exposed to two concentrations of HF-HQ.
2012-02-03 | GSE35360 | GEO