Example data for ESI-Orbitrap IRMS
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ABSTRACT:
INSTRUMENT(S): ESI-Orbitrap Exploris 240 Isotope Solutions
ORGANISM(S): Nitrate
SUBMITTER: 
Cajetan Neubauer
PROVIDER: MSV000092246 | MassIVE | Thu Jun 22 20:40:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:Data analyzed within Procedure 2 in Kantnerova et al. 202X in Nature Protocols. Procedure 2 describes the stable isotope analysis of the model analyte nitrate (NO3-) by applying the flow injection using an HPLC system with an autosampler.
The nitrate data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions.
Sample = USGS32, Reference = USGS35 (nitrate isotopic reference materials from the United States Geological Survey), 50 uM nitrate in methanol.
Isotopocule data collected "with M0" base peak.
RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input.
There are three datasets with the following prefixes (to be removed before re-analysis using the IsoX software and the R scripts):
"01_" - USGS32 vs USGS35, optimal ion source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements
"02_" - USGS32 vs USGS35, non-optimal ion-source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements
"03_" - USGS32 vs USGS35, alternating injections of USGS35 and USGS32 extended to a total of 315 injections
2023-08-17 | MSV000092683 | MassIVE
Project description:Data analyzed within Procedure 2 in Kantnerova et al. 2024 in Nature Protocols (https://doi.org/10.1038/s41596-024-00981-5). Procedure 2 describes the stable isotope analysis of the model analyte nitrate (NO3-) by applying the flow injection using an HPLC system with an autosampler. The nitrate data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions. Sample = USGS32, Reference = USGS35 (nitrate isotopic reference materials from the United States Geological Survey), 50 uM nitrate in methanol. Isotopocule data collected "with M0" base peak. RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input. There are three datasets with the following prefixes: "01_" - USGS32 vs USGS35, optimal ion source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements "02_" - USGS32 vs USGS35, non-optimal ion-source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements "03_" - USGS32 vs USGS35, alternating injections of USGS35 and USGS32 extended to a total of 315 injections. Before rerunning the IsoX data analysis, remove the prefixes "01_", "02_" and "03_" from the respective .tsv files.
2023-11-01 | MSV000093223 | MassIVE
Project description:Data analyzed within Procedure 1 in Kantnerova et al. 202X in Nature Protocols.
Procedure 1 describes a direct infusion analysis using an easily accessible Orbitrap MS calibration solution FlexMix, analyzing its two compounds: a) trifluoroacetate (TFA) in the negative ESI mode, and b) the peptide MRFA (Met-Arg-Phe-Ala) and its amino acid fragments (MS/MS analysis) in the positive ESI mode.
The TFA data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions.
The MRFA data were collected using a Thermo Scientific Orbitrap Exploris 480 Isotope Solutions.
RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input. Before rerunning the IsoX data analysis, remove the suffixes "_TFA" and "_MRFA" from the respective .tsv files.
2023-08-11 | MSV000092644 | MassIVE
Project description:Data analyzed within Procedure 1 in Kantnerova et al. 2024 in Nature Protocols (https://doi.org/10.1038/s41596-024-00981-5). Procedure 1 describes a direct infusion analysis using an easily accessible Orbitrap MS calibration solution FlexMix, analyzing its two compounds: a) trifluoroacetate (TFA) in the negative ESI mode, and b) the peptide MRFA (Met-Arg-Phe-Ala) and its amino acid fragments (MS/MS analysis) in the positive ESI mode. The TFA data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions. The MRFA data were collected using a Thermo Scientific Orbitrap Exploris 480 Isotope Solutions. RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input. Before rerunning the IsoX data analysis, remove the suffixes "_TFA", "_MRFA" and "_MRFA_2" from the respective .tsv files.
2023-11-01 | MSV000093222 | MassIVE
Project description:Pancreatic Cancer (PC) remains highly lethal due to limited therapeutic options. Here we utilize a genomic-data-driven Connectivity Mapping (CMAP) to identify a drug closer to real-world PC targeting. ISOX emerged as a top potential drug from the CMAP pipeline across human PC tissues, cell lines, tumoroids, and patient-derived xenografts datasets. Here, we use PC cells, human and mouse tumoroids, and in vivo mouse models to test the ability of ISOX alone and in combination with 5FU to inhibit tumor growth. Transcriptomic and pathway analysis of the ISOX-LINCS signature identified the various pathways as targets for ISOX, suggesting a multiple-target action. Specifically, we discovered that genetic and pharmacological targeting of HDAC6 affected non-histone protein cMYC acetylation leading to cMYC instability, thereby disrupting PC stem cells. Finally, KrasG12D harboring organoids and mice responded effectively against ISOX and 5FU treatment by enhancing survival and controlling metastasis incidence. Overall, our data validate ISOX as a novel drug to treat advanced PC patients without toxicity to normal cells
2024-03-13 | GSE240597 | GEO
Project description:This data set contains ChEC-seq binding profiles of various TF in yeast strains deleted of other TFs. Each sample has a pair-end sequencing file and a processed file (.out) is a genomic signal track after alignment to S.cerevisiae (R64) reference genome. Mapping was done using the read end. This dataset also contains raw and processed MNase-seq data files for nucleosome occupancy. Data related to manuscript: The architecture of binding cooperativity between densely bound transcription factors.
2023-08-01 | GSE222268 | GEO
Project description:Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. In this work, we performed gene expression analysis in the root of the model plant for C3 grasses Brachypodiyum distachyon, reference accession Bd21, grown with exclusive NH4+ or NO3- supply.
2024-09-05 | GSE275962 | GEO
Project description:Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.
2019-12-31 | GSE112437 | GEO
Project description:Nitrate (NO3-) is crucial for optimal plant growth and development and often limits crop productivity at the low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO3- acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE). Here, we demonstrated that NO3--inducible ZmNRT1.1B (ZmNPF6.6) positively regulated NO3--dependent growth and NUE in maize. We showed that the tandem duplicated proteoform ZmNRT1.1C is irrelevant to maize seedling growth under nitrate supply, however, loss-of-function of ZmNRT1.1B significantly weakened plant growth under adequate NO3- supply in both hydroponic and field conditions. 15N-labeled NO3- absorption assay indicated that ZmNRT1.1B mediated high-affinity NO3--transport and root-to-shoot NO3- translocation. Furthermore, upon NO3- supply, ZmNRT1.1B promotes cytoplasmic-to-nuclear shuttling of ZmNLP3.1 (ZmNLP8), which co-regulates the expression of genes involved in NO3- response, cytokinin biosynthesis and carbon metabolism. Remarkably, overexpression of ZmNRT1.1B in modern maize hybrids improved grain yield under nitrogen (N) limiting fields. Taken together, our study revealed a crucial role of ZmNRT1.1B in high-affinity NO3- transport and signaling and offers valuable genetic resource for breeding nitrogen use efficient high-yield cultivars.
2023-04-25 | GSE227472 | GEO
Project description:Processing of crude drug is a key character of traditional Chinese medicine (TCM), which could enhance the efficacy and/or reduce the toxicity of crude drugs to fulfill different requirements of TCM clinical practice. Epimedii folium (EF) is a widely used TCM. As a traditional method of TCM, EF is processed with refined mutton fat before being used in clinical practice. It has been reported that processing EF with mutton fat could improve the bioavailability and intestinal absorption of epimedium flavonoids and thus enhances the pharmacological effects. For economic benefits, it is possible to adulterate processed EF with unprocessed drug or process EF with cheaper plant oils. In the present study, 17 batches of crude and processed EF samples were collected from the Chinese market and 10 batches of replica processed drugs were prepared with different edible plant oils and animal fats in our laboratory. Elemental analyzer coupled with isotopic ratio mass spectrometry (EA-IRMS) was applied to determine the ? 13C values of the cyclohexane extracts of those samples. Significant differences could be observed in the results. EA-IRMS could be used to discriminate raw EF, processed EF, and EF processed with C3 plant oils.
| S-EPMC7023830 | biostudies-literature