Summary of Study ST001095

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 PR000733. The data can be accessed directly via it's Project DOI: 10.21228/M8XM40 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001095
Study TitleData resource for fully 13C labelled and non-labelled plant tissues (part-I)
Study SummaryLC-MS/MS data files of fully 13C labelled and 12C plant tissues, which were utilized to determine the carbon element number for metabolite characterizations.
Institute
RIKEN
DepartmentCenter for Sustainable Resource Science
LaboratoryMetabolome Informatics Research Team
Last NameTsugawa
First NameHiroshi
Address1-7-22 Suehiro-cho, Tsurumi-ku
Emailhiroshi.tsugawa@riken.jp
Phone+81-45-503-9618
Submit Date2018-11-08
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Hiroshi Tsugawa Hiroshi Tsugawa
https://dx.doi.org/10.21228/M8XM40
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000733
Project DOI:doi: 10.21228/M8XM40
Project Title:Computational metabolomics to characterize metabolites in stable isotope-labelled organisms.
Project Summary:We developed a computational metabolomics workflow to characterize metabolite structures by using the set of fully 13C-labelled and non-labelled LC-MS/MS data. The platform was applied to structure elucidations for 31 tissues of 12 plant species, resulting in the assignments of 1,092 structures and 344 formulas to 3,604 carbon-determined metabolite ions. We also applied the methodology to find the trait-metabolite associations in natural accessions of Arabidopsis thaliana.
Institute:RIKEN
Department:Center for Sustainable Resource Science
Laboratory:Metabolome Informatics Research Team
Last Name:Tsugawa
First Name:Hiroshi
Address:1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
Email:hiroshi.tsugawa@riken.jp
Phone:+81-45-503-9618

Subject:

Subject ID:SU001139
Subject Type:Plant
Subject Species:Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra
Subject Comments:Allium cepa/Arabidopsis thaliana/Glycine max/Glycyrrhiza glabra/Glycyrrhiza urahensis/Medicago truncatula/Nicotiana tabacum/Ophiorrhiza pumila/Oryza sativa/Solanum lycopersicum/Solanum tuberosum/Zea mays

Factors:

Subject type: Plant; Subject species: Allium cepa;Arabidopsis thaliana;Glycine max;Glycyrrhiza glabra (Factor headings shown in green)

mb_sample_id local_sample_id Label Species SampleSource
SA07455612C-AC-BulbNon-labelled Allium cepa bulb
SA07455712C-AC-LeafNon-labelled Allium cepa leaf
SA07455812C-AC-RootNon-labelled Allium cepa root
SA07455912C-AT-LeafAndStemNon-labelled Arabidopsis thaliana leaf&stem
SA07456012C-AT-RootNon-labelled Arabidopsis thaliana root
SA07456112C-GM-LeafAndStemNon-labelled Glycine max leaf&stem
SA07456212C-GM-RootNon-labelled Glycine max root
SA07456312C-GG-LeafAndStemNon-labelled Glycyrrhiza glabra leaf&stem
SA07456412C-GG-RootNon-labelled Glycyrrhiza glabra root
SA07456512C-GU-LeafAndStemNon-labelled Glycyrrhiza uralensis leaf&stem
SA07456612C-GU-RootNon-labelled Glycyrrhiza uralensis root
SA07456712C-MT-FlowerNon-labelled Medicago truncatula flower
SA07456812C-MT-LeafAndStemNon-labelled Medicago truncatula leaf&stem
SA07456912C-MT-RipePodNon-labelled Medicago truncatula ripe pod
SA07457012C-MT-RootNon-labelled Medicago truncatula root
SA07457112C-MT-SeedNon-labelled Medicago truncatula seed
SA07457212C-NT-LeafAndStemNon-labelled Nicotiana tabacum leaf&stem
SA07457312C-NT-RootNon-labelled Nicotiana tabacum root
SA07457412C-OP-RootNon-labelled Ophiorrhiza pumila root
SA07457512C-OS-LeafAndStemNon-labelled Oryza sativa leaf&stem
SA07457612C-OS-RootNon-labelled Oryza sativa root
SA07457712C-SL-FruitGreenNon-labelled Solanum lycopersicum fruit green
SA07457812C-SL-LeafAndSLemNon-labelled Solanum lycopersicum leaf&stem
SA07457912C-SL-RipeNon-labelled Solanum lycopersicum ripe
SA07458012C-ST-LeafAndStemNon-labelled Solanum tuberosum leaf&stem
SA07458112C-ST-RootNon-labelled Solanum tuberosum root
SA07458212C-ST-TuberNon-labelled Solanum tuberosum tuber
SA07458312C-ZM-LeafNon-labelled Zea mays leaf
SA07458412C-ZM-RootNon-labelled Zea mays root
SA07458512C-ZM-SeedNon-labelled Zea mays seed
SA07458612C-ZM-StemNon-labelled Zea mays stem
SA07458713C-AC-BulbU-13C Allium cepa bulb
SA07458813C-AC-LeafU-13C Allium cepa leaf
SA07458913C-AC-RootU-13C Allium cepa root
SA07459013C-AT-LeafAndStemU-13C Arabidopsis thaliana leaf&stem
SA07459113C-AT-RootU-13C Arabidopsis thaliana root
SA07459213C-GM-LeafAndStemU-13C Glycine max leaf&stem
SA07459313C-GM-RootU-13C Glycine max root
SA07459413C-GG-LeafAndStemU-13C Glycyrrhiza glabra leaf&stem
SA07459513C-GG-RootU-13C Glycyrrhiza glabra root
SA07459613C-GU-LeafAndStemU-13C Glycyrrhiza uralensis leaf&stem
SA07459713C-GU-RootU-13C Glycyrrhiza uralensis root
SA07459813C-MT-FlowerU-13C Medicago truncatula flower
SA07459913C-MT-LeafAndStemU-13C Medicago truncatula leaf&stem
SA07460013C-MT-RipePodU-13C Medicago truncatula ripe pod
SA07460113C-MT-RootU-13C Medicago truncatula root
SA07460213C-MT-SeedU-13C Medicago truncatula seed
SA07460313C-NT-LeafAndStemU-13C Nicotiana tabacum leaf&stem
SA07460413C-NT-RootU-13C Nicotiana tabacum root
SA07460513C-OP-RootU-13C Ophiorrhiza pumila root
SA07460613C-OS-LeafAndStemU-13C Oryza sativa leaf&stem
SA07460713C-OS-RootU-13C Oryza sativa root
SA07460813C-SL-FruitGreenU-13C Solanum lycopersicum fruit green
SA07460913C-SL-LeafAndSLemU-13C Solanum lycopersicum leaf&stem
SA07461013C-SL-RipeU-13C Solanum lycopersicum ripe
SA07461113C-ST-LeafAndStemU-13C Solanum tuberosum leaf&stem
SA07461213C-ST-RootU-13C Solanum tuberosum root
SA07461313C-ST-TuberU-13C Solanum tuberosum tuber
SA07461413C-ZM-LeafU-13C Zea mays leaf
SA07461513C-ZM-RootU-13C Zea mays root
SA07461613C-ZM-SeedU-13C Zea mays seed
SA07461713C-ZM-StemU-13C Zea mays stem
Showing results 1 to 62 of 62

Collection:

Collection ID:CO001133
Collection Summary:Leaf/stem and root tissues of Arabidopsis thaliana, Nicotiana tabacum, Glycine max, Glycyrrhiza glabra, Glycyrrhiza urahensis, and Oryza sativa, bulb, leaf, and root tissues of Allium cepa, flower, leaf/stem, seed pod, seed, and root tissues of Medicago truncatula, green and ripe fruit-, and leaf/stem tissues of Solanum lycopersicum, leaf/stem, root, and tuber tissues of Solanum tuberosum, and leaf, stem, seed, and root tissues of Zea mays were purchased from IsoLife Co. (Wageningen UR, Netherlands). The hairy root of Ophiorrhiza pumila was grown as follows. O. pumila hairy roots were derived and maintained, except for the carbon source. We supplied 1.5% D-glucose instead of 1.5% sucrose. We obtained 4-week-old O. pumila hairy roots and sub-cultured them in 1.5% D-glucose (U-13C6, 99%) (Cambridge Isotope Laboratories, Inc.) for two generations for complete isotope labeling of the metabolome. Hairy roots from the same batch used for isotope-labeling were sub-cultured for two subcultures in 1.5% D-glucose (Nacalai Tesque, Inc); they served as the control. Hairy roots from the second sub-culture of sub-cultured tissues growing in 1.5% isotope-labelled or un-labelled 1.5% D-glucose were harvested, wiped with paper towels and snap-frozen in liquid-N2.
Sample Type:Plant

Treatment:

Treatment ID:TR001153
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001146
Sampleprep Summary:Samples (3 mg) of dried plant tissues were weighted in a 2.0-ml microtube (Sarstedt). Their metabolites were extracted with 150 µl of 80% MeOH containing 2.5 µM lidocaine and 10-camphour sulfonic acid per mg of dry weight using a mixer-mill with zirconia beads [7 min at 18 Hz and 4 degree C (MM300; Retsch)]. After 10-min centrifugation at 17,800 g the supernatant was filtered using an HLB µElution plate (Waters).

Combined analysis:

Analysis ID AN001781 AN001782
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2.1mm,1.7um) Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH001259
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:99.5% solvent A/0.5% solvent B at 0 min, 99.5%A/0.5%B at 0.1 min, 20%A/80%B at 10 min, 0.5%A/99.5%B at 10.1 min, 0.5%A/99.5%B at 12.0 min, 99.5%A/0.5%B at 12.1 min and 99.5%A/0.5%B at 15.0 min
Flow Rate:0.3 ml/min at 0 min, 0.3 ml/min at 10 min, 0.4 ml/min at 10.1 min, 0.4 ml/min at 14.4 min, and 0.3 ml/min at 14.5 min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001645
Analysis ID:AN001781
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:+3.00 kV
Collision Energy:6 V
Source Temperature:120
Dataformat:.raw
Desolvation Gas Flow:800 l/hr
Desolvation Temperature:450 degree C
Scan Range Moverz:50 - 1500
  
MS ID:MS001646
Analysis ID:AN001782
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:-2.75 kV
Collision Energy:6 V
Source Temperature:120
Dataformat:.raw
Desolvation Gas Flow:800 l/hr
Desolvation Temperature:450 degree C
Scan Range Moverz:50 - 1500
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