GNPS - Metabolomics profiling using mouse Circadian Rhythm
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 120
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
ANDREW DAVID Patterson
PROVIDER: MSV000098103 | GNPS | Mon Jun 09 10:55:00 BST 2025
REPOSITORIES: GNPS
Similar Datasets
Project description:Those data were generated from multiple organs and contents of mouse focusing on circadian rhythm. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 120 for bile acids profiling. Chromatographic separation was performed on a Waters BEH C8 UHPLC column 100 x 2.1 mm.
2025-06-09 | MSV000098103 | MassIVE
Project description:We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training. The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice.
2013-03-24 | GSE44229 | GEO
Project description:We profiled lipids across multiple organs and biofluids from C57BL/6NCrl (B6NCrl-MVP) wild-type mice at two ages (16 and 92 weeks), including both sexes. Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Lipidomics was performed by LC-MS/MS on a Thermo Scientific Orbitrap Exploris 240 coupled to a Vanquish UHPLC in both positive and negative ion modes. Analytes were separated on a Waters ACQUITY Premier BEH C18 column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.
2025-10-05 | MSV000099388 | MassIVE
Project description:We profiled polar metabolites across multiple organs and fluids from C57BL/6NCrl (B6NCrl-MVP) wild-type mice at two ages (16 and 92 weeks), including both sexes. Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Polar metabolomics was performed by LC-MS/MS on a Thermo Scientific Q Exactive HF-X Quadrupole-Orbitrap coupled to a Vanquish UHPLC in positive mode. Metabolites were separated on a Waters ACQUITY Premier BEH Amide column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.
2025-10-05 | MSV000099387 | MassIVE
Project description:We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training. The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice. Examination of gene expression following a learning event in wildtype and Baf53b+/- mutant mice in dorsal hippocampus.
2013-03-24 | E-GEOD-44229 | biostudies-arrayexpress
Project description:Pretreated human follicular fluid was prepared for targeted metabolomics experiments. For this purpose, 12-point standard calibration curves in the respective range with reference material were measured, and the limit of detection (LOD) and limit of quantification (LOQ) for each neurotransmitter under investigation were calculated. LC-MS/MS was conducted by an ultra-performance liquid chromatography method using a Waters ACQUITY UPLC BEH C18 column (2.1 mm×100 mm, 1.7 µm, Waters, USA). The Waters acquisition UPLC was coupled to an API 4000 triple quadrupole mass spectrometer (AB SCIEX, USA). The mobile phase A buffer was 10% methanol in water (containing 0.1% formic acid), and the mobile phase B buffer was 50% methanol in water (containing 0.1% formic acid). The LC gradient elution was at a flow rate of 0.3 mL/min at 0-8.0 min and 0.4 ml/min at 8.0-17.5 min, then 10%-30% B at 0-6.5 min; 30%-100% B at 6.5-7 min; 100% B at 7-14min; and 100%-10% B at 14-17.5min. The injection volume was 5 µl and the column temperature was set to 40 °C. Twenty-three metabolites (Ach: Acetylcholine chloride; Gln: Glutamine; Glu: Glutamate; His: L-Histidine; NE: norepinephrine; Tyr:Tyrosine; Trp:Tryptophan; Kyn: Kynurenine; GABA: 4-Aminobutyric acid;HisA:Histamine; PA:Picolinic acid;TyrA:Tyramine;DA:Hydroxytyramine hydrochloride; TrpA:Tryptamine;5-HT:Serotonin hydrochloride;E:Adrenaline hydrochloride;KynA:Kynurenic acid;5-HIAA:5-Hydroxyindole-3-acetic acid;DOPA:Levodopa;XA:Xanthurenic acid;VWA:Vanillymandelic Acid; 5-HTTP:5-Hydroxytryptophan;MT:Melatonine)were simultaneously reported in LC-MS/MS multiple reaction monitoring (MRM) mode. Data analysis was performed with Analyst 1.6 software.
2022-08-12 | PXD031560 | Pride
Project description:The aim of this study was to identify chemoresistance-associated genes in hepatocellular carcinoma (HCC). cDNA microarray analysis was performed to compare the mRNA expression profiles of a human metastatic HCC cell line (named MHCC97Low) and its derived chemoresistant sublines including cisplatin resistant subline (named MHCC97L/CisR or C8) and doxorubicin resistant subline (named MHCC97L/DoxR or D5). Total RNAs were extracted from MHCC97Low (97Low as sample name), MHCC97L/CisR (C8 as sample name) and MHCC97L/DoxR (D5 as sample name), and hybridized on Affymetrix microarrays. We planed to identify differential genes between 97Low and C8 (cisplatin resistant genes) as well as to identify differential genes between 97Low and D5 (doxorubicin resistant genes).
2014-01-17 | E-GEOD-54175 | biostudies-arrayexpress
Project description:Analyses of 9 Brazilian Malpighiaceae species (leaves). Dried plant material were extracted, with EtOH80%. Positive and Negative ionization mode analises. LC-MS/MS performed in an Waters Acquity UPLC H-Class (Waters) using a Acquity BEH Shield RP18 reverse phase UHPLC column (1.7 um, 100 x 2.1 mm) and Xevo G2-XS QToF Mass Spectrometer (Waters) equipped with ESI source.
2020-03-19 | MSV000085121 | GNPS
Project description:In this work, we evaluate the performance of nonporous C-18 stationary phases in high-speed proteomics workflows. We employed two commercially available sub-2 µm nonporous particle (NPP) materials, ODSIIIE and SOLAD, to fabricate analytical columns using 150 µm internal diameter (i.d.) fused silica capillaries to ensure compatibility with nano-UHPLC and nano-HPLC pressure regimes. Using long NPP columns (15 – 25 cm) connected to a conventional nano-UHPLC, we found that both materials supported efficient peptide separations within the flow rate and pressure ranges typical of nano-UHPLC systems. Shorter columns (4 – 5 cm), used with the 10- and 16-minute Whisper Zoom 120 and Zoom 80 methods on the Evosep One HPLC, demonstrated competitive separation performance compared to columns packed with fully porous (FPP) and superficially porous particles (SPP), achieving full-width at half maximum (FWHM) values below 2 seconds (Zoom 120) and 3 seconds (Zoom 80). Peak shape remained consistent with sample loads up to 25 ng of a human cell lysate digest, a level well-suited to the sensitivity of modern mass spectrometers. DIA LC-MS/MS analysis of 20 ng from the same digest demonstrated that NPP columns provided comparable or superior performance relative to FPP and SPP materials, identifying approximately 23,000 precursors (~3,000 proteins) with Zoom 120 and ~33,000 precursors (~3,800 proteins) with Zoom 80. These findings establish NPP-based columns as a viable and competitive alternative to FPP and SPP materials, particularly suited for high-throughput and high-sensitivity proteomics applications.
2025-08-27 | PXD064019 | Pride
Project description:Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain. Here, we presented global circadian transcript profile of mouse tissues (i.e. skeletal muscle) entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.
2023-04-23 | GSE194106 | GEO