Summary of study ST001613

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001033. The data can be accessed directly via it's Project DOI: 10.21228/M85M45 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001613
Study TitleComparing gas chromatography with time-of-flight, quadrupole time-of-light and quadrupole mass spectrometry for stable isotope tracing (part-II)
Study SummaryStable isotope tracers are applied in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) due to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well-studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. Overall, all three GC-MS instruments (low-resolution GC-SQ-MS, low-resolution GC-TOF-MS, and high-resolution GC-Q-TOF-MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, TCA metabolites and amino acids, yielding similar biological results, with high-resolution GC-Q-TOF-MS offering additional capabilities to identify chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.
Institute
University of California, Davis
Last NameZhang
First NameYing
Address451 East Health Science Drive, Davis, CA, 95616, USA
Emailythzhang@ucdavis.edu
Phone1-530-752-8129
Submit Date2020-11-05
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailGC-MS
Release Date2020-12-10
Release Version1
Ying Zhang Ying Zhang
https://dx.doi.org/10.21228/M85M45
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001033
Project DOI:doi: 10.21228/M85M45
Project Title:Comparing gas chromatography with time-of-flight, quadrupole time-of-light and quadrupole mass spectrometry for stable isotope tracing
Project Summary:Stable isotope tracers are applied in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) due to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well-studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. Overall, all three GC-MS instruments (low-resolution GC-SQ-MS, low-resolution GC-TOF-MS, and high-resolution GC-Q-TOF-MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, TCA metabolites and amino acids, yielding similar biological results, with high-resolution GC-Q-TOF-MS offering additional capabilities to identify chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.
Institute:UC Davis
Laboratory:Oliver Fiehn
Last Name:Ying
First Name:Zhang
Address:West Coast Metabolomics Center, University of California, Davis
Email:ythzhang@ucdavis.edu
Phone:+1-530-754-8258

Subject:

Subject ID:SU001690
Subject Type:Bacteria
Subject Species:Rothia mucilaginosa
Taxonomy ID:43675
Genotype Strain:RmFLR01

Factors:

Subject type: Bacteria; Subject species: Rothia mucilaginosa (Factor headings shown in green)

mb_sample_id local_sample_id Condition Collection Time
SA136818171015bBG_41_010_1Ambient 12h
SA136819171015bBG_42_010_1Ambient 12h
SA136820171015bBG_41_009_1Ambient 12h
SA136821171015bBG_41_008_1Ambient 12h
SA136822171015bBG_41_006_1Ambient 12h
SA136823171015bBG_41_007_1Ambient 12h
SA136824171015bBG_42_009_1Ambient 12h
SA136825171015bBG_42_003_1Ambient 12h
SA136826171015bBG_41_005_1Ambient 12h
SA136827171015bBG_42_002_1Ambient 12h
SA136828171015bBG_42_004_1Ambient 12h
SA136829171015bBG_42_005_1Ambient 12h
SA136830171015bBG_42_007_1Ambient 12h
SA136831171015bBG_42_006_1Ambient 12h
SA136832171015bBG_42_008_1Ambient 12h
SA136833171015bBG_40_003_1Ambient 12h
SA136834171015bBG_40_007_1Ambient 12h
SA136835171015bBG_40_006_1Ambient 12h
SA136836171015bBG_40_008_1Ambient 12h
SA136837171015bBG_40_009_1Ambient 12h
SA136838171015bBG_42_001_1Ambient 12h
SA136839171015bBG_40_010_1Ambient 12h
SA136840171015bBG_40_005_1Ambient 12h
SA136841171015bBG_40_004_1Ambient 12h
SA136842171015bBG_41_002_1Ambient 12h
SA136843171015bBG_41_003_1Ambient 12h
SA136844171015bBG_41_001_1Ambient 12h
SA136845171015bBG_40_001_1Ambient 12h
SA136846171015bBG_40_002_1Ambient 12h
SA136847171015bBG_41_004_1Ambient 12h
SA136848171015bBG_43_009_1Ambient 24h
SA136849171015bBG_45_001_1Ambient 24h
SA136850171015bBG_45_002_1Ambient 24h
SA136851171015bBG_44_001_1Ambient 24h
SA136852171015bBG_44_002_1Ambient 24h
SA136853171015bBG_44_004_1Ambient 24h
SA136854171015bBG_44_003_1Ambient 24h
SA136855171015bBG_45_003_1Ambient 24h
SA136856171015bBG_45_004_1Ambient 24h
SA136857171015bBG_43_010_1Ambient 24h
SA136858171015bBG_45_010_1Ambient 24h
SA136859171015bBG_45_008_1Ambient 24h
SA136860171015bBG_45_007_1Ambient 24h
SA136861171015bBG_45_005_1Ambient 24h
SA136862171015bBG_45_006_1Ambient 24h
SA136863171015bBG_44_005_1Ambient 24h
SA136864171015bBG_45_009_1Ambient 24h
SA136865171015bBG_44_006_1Ambient 24h
SA136866171015bBG_43_004_1Ambient 24h
SA136867171015bBG_43_006_1Ambient 24h
SA136868171015bBG_43_007_1Ambient 24h
SA136869171015bBG_43_008_1Ambient 24h
SA136870171015bBG_43_003_1Ambient 24h
SA136871171015bBG_43_005_1Ambient 24h
SA136872171015bBG_44_008_1Ambient 24h
SA136873171015bBG_43_002_1Ambient 24h
SA136874171015bBG_44_009_1Ambient 24h
SA136875171015bBG_44_007_1Ambient 24h
SA136876171015bBG_44_010_1Ambient 24h
SA136877171015bBG_43_001_1Ambient 24h
SA136878171012bBG_34_010_1Ambient 4h
SA136879171012bBG_34_009_1Ambient 4h
SA136880171012bBG_35_001_1Ambient 4h
SA136881171012bBG_35_003_1Ambient 4h
SA136882171012bBG_35_004_1Ambient 4h
SA136883171012bBG_35_002_1Ambient 4h
SA136884171012bBG_34_002_1Ambient 4h
SA136885171012bBG_34_003_1Ambient 4h
SA136886171012bBG_35_006_1Ambient 4h
SA136887171012bBG_34_004_1Ambient 4h
SA136888171012bBG_34_005_1Ambient 4h
SA136889171012bBG_34_007_1Ambient 4h
SA136890171012bBG_34_006_1Ambient 4h
SA136891171012bBG_34_008_1Ambient 4h
SA136892171012bBG_36_007_1Ambient 4h
SA136893171012bBG_36_004_1Ambient 4h
SA136894171012bBG_36_005_1Ambient 4h
SA136895171012bBG_36_003_1Ambient 4h
SA136896171012bBG_36_002_1Ambient 4h
SA136897171012bBG_34_001_1Ambient 4h
SA136898171012bBG_36_001_1Ambient 4h
SA136899171012bBG_36_006_1Ambient 4h
SA136900171012bBG_36_008_1Ambient 4h
SA136901171012bBG_35_009_1Ambient 4h
SA136902171012bBG_35_008_1Ambient 4h
SA136903171012bBG_35_010_1Ambient 4h
SA136904171012bBG_36_010_1Ambient 4h
SA136905171012bBG_36_009_1Ambient 4h
SA136906171012bBG_35_007_1Ambient 4h
SA136907171012bBG_35_005_1Ambient 4h
SA136908171012bBG_37_010_1Ambient 8h
SA136909171012bBG_37_009_1Ambient 8h
SA136910171012bBG_38_001_1Ambient 8h
SA136911171012bBG_38_002_1Ambient 8h
SA136912171012bBG_38_004_1Ambient 8h
SA136913171012bBG_38_003_1Ambient 8h
SA136914171012bBG_37_008_1Ambient 8h
SA136915171012bBG_37_007_1Ambient 8h
SA136916171012bBG_37_002_1Ambient 8h
SA136917171012bBG_39_010_1Ambient 8h
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 268

Collection:

Collection ID:CO001683
Collection Summary:A quality control mixture of 29 unlabeled metabolite standards (Supporting information Table SI 1) was prepared to reach a final concentration of 1 mg/mL as stock solution. 50 µL aliquot from each stock solution was combined into a new tube and dried down. Then, the mixture was diluted to reach a final concentration of 50 µg/mL working solution. Rothia mucilaginosa strain RmFLR01 was isolated from a cystic fibrosis (CF) patient at the UC San Diego Adult CF Clinic [19, 32]. R. mucilaginosa cultures were grown in triplicates in artificial-sputum medium [33] spiked with 100 mM [U-13C6] d-glucose (Cambridge Isotope Laboratory, Tewksbury, MA, USA) under anaerobic and aerobic conditions (5% CO2) at 37°C and harvested at 4, 8, 12 and 24 h for isotope tracer analyses.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001703
Treatment Summary:under anaerobic and aerobic conditions (5% CO2) at 37°C and harvested at 4, 8, 12 and 24 h for isotope tracer analyses

Sample Preparation:

Sampleprep ID:SP001696
Sampleprep Summary:For the 29 unlabeled standards mixture, 10 µL of the final solution was dried down for GC-MS measurement. Derivatization and data acquisition of mixture aliquots by GC-MS were reproduced on three days for inter-day precision. Dried mixtures were derivatized by adding 10 µL of 40 mg/mL methoxyamine hydrochloride (Sigma-Aldrich, St. Louis, MO, USA) in pyridine (Sigma-Aldrich, St. Louis, MO, USA) and shaking at 30°C for 1.5 h. Subsequently, 90 µL MTBSTFA (Sigma-Aldrich, St. Louis, MO, USA) was added with 13 fatty acid methyl esters (FAMEs) as retention index markers and shaken at 80°C for 30 min. Samples were immediately transferred to crimp top vials and injected onto each GC-MS instrument. Same samples of R. mucilaginosa cultures were extracted using published methods [19]. Samples were added 1 mL pre-chilled, degassed acetonitrile: isopropanol: water (v/v/v 3:3:2, Fisher Scientific) followed by vortexing 30 s and shaking at 4°C for 5 min. Samples were centrifuged for 2 min at 12,210 × g to precipitate debris from extracts. Supernatants were collected and split into two equal portions. One aliquot was dried to completeness in a Labconco cold trap centrifuge evaporator and then resuspended in 0.5 mL degassed acetonitrile: water (v/v 1:1, Fisher Scientific) to remove triacylglycerides. Resuspension solutions were vortexed for 30s and centrifuged for 2 min. Supernatants were transferred into clean Eppendorf tubes and dried down completely. Dried extracts were derivatized as given above.

Combined analysis:

Analysis ID AN002648
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus IV GC
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units peak height

Chromatography:

Chromatography ID:CH001956
Chromatography Summary:untargeted metabolomics metadata
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002460
Analysis ID:AN002648
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:LECO TOF-MS raw data files (.CDF format) were converted to MassHunter formats (.D format) using Agilent GCMS translator software. MassHunter Quantitative Analysis B.07.00 version was used to process the data
Ion Mode:POSITIVE
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