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Protocols

PRIMe specifications

Information


Unique identifier OMICS_19222
Name PRIMe
Alternative name Platform for RIKEN Metabolomics
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Content license CC Attribution
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Tetsuya Sakurai

Publications for Platform for RIKEN Metabolomics

PRIMe citations

 (9)
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Nitrite Derived from Endogenous Bacterial Nitric Oxide Synthase Activity Promotes Aerobic Respiration

2017
MBio
PMCID: 5539425
PMID: 28765220
DOI: 10.1128/mBio.00887-17
call_split See protocol

[…] cing and normalization of NMR peak intensities. NMR peaks from the 2D 1H-13C HSQC spectra were annotated by comparing the observed 1H and 13C chemical shifts to the metabolite reference data from the Platform for RIKEN Metabolomics (PRIMe) (), Human Metabolome Database (HMDB) (), Madison metabolomics Consortium Database (), Metabominer (), and BiomagResBank (BMRB) () with error tolerances of 0.08  […]

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Rapid discrimination of strain dependent fermentation characteristics among Lactobacillus strains by NMR based metabolomics of fermented vegetable juice

2017
PLoS One
PMCID: 5536307
PMID: 28759594
DOI: 10.1371/journal.pone.0182229
call_split See protocol

[…] , 2D NMR spectra were measured on an Avance-800 spectrometer (Bruker BioSpin) at proton and carbon frequencies of 800.33 and 201.24 MHz, respectively. The SpinAssign program at the PRIMe web service (Platform for RIKEN Metabolomics: http://prime.psc.riken.jp/) was used for annotating metabolite signals in HSQC spectra. Peak tables of HSQC spectra were generated using NMRPipe and NMRDraw as describ […]

library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] ng; PCA: principal component analysis; PlantMAT: Plant Metabolite Annotation Toolbox; PLS-DA: partial least squares discriminant analysis; PMR: Plant/Eukaryotic and Microbial Systems Resource; PRIMe: Platform for RIKEN Metabolomics; RAMSY: Ratio Analysis of Mass Spectrometry; ReSpect: RIKEN MSn Spectral Database for Phytochemicals; SDBS: Spectral Database for Organic Compounds; SIRIUS: Sum Formula […]

call_split

Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression

2017
MBio
PMCID: 5312079
PMID: 28196956
DOI: 10.1128/mBio.01434-16
call_split See protocol

[…] cing and normalization of NMR peak intensities. NMR peaks from the 2D 1H-13C HSQC spectra were annotated by comparing the observed 1H and 13C chemical shifts to the metabolite reference data from the Platform for RIKEN metabolomics (PRIMe; http://prime.psc.riken.jp/) (), Human Metabolome Database (HMDB; http://www.hmdb.ca/) (), Madison metabolomics Consortium Database (http://mmcd.nmrfam.wisc.edu/ […]

library_books

Dietary intake of heat killed Lactococcus lactis H61 delays age related hearing loss in C57BL/6J mice

2016
Sci Rep
PMCID: 4802309
PMID: 27000949
DOI: 10.1038/srep23556

[…] m was processed with NMRPipe and analysed using NMRDraw to generate a peak table; metabolite annotation was performed by applying the peak table to a SpinAssign program through the PRIMe web service (Platform for RIKEN Metabolomics; http://prime.psc.riken.jp/). Other public databases, such as the Human Metabolomics Database (http://www.hmdb.ca/) and the Biological Magnetic Resonance Data Bank (htt […]

library_books

Unified and Isomer Specific NMR Metabolomics Database for the Accurate Analysis of 13C–1H HSQC Spectra

2014
ACS Chem Biol
PMCID: 4340359
PMID: 25333826
DOI: 10.1021/cb5006382

[…] olomics databases, each with its own query algorithm, are the BMRB (Biological Magnetic Resonance Data Bank), HMDB (Human Metabolome Database), MMCD (Madison Metabolomics Consortium Database), PRIMe (Platform for RIKEN Metabolomics) database, and the Metabominer database. All of these databases were compiled by recording the 2D 13C–1H HSQC spectra of solutions of isolated (pure) compounds and they […]

Citations

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PRIMe institution(s)
RIKEN Plant Science Center, Yokohama, Japan; Organization of Advanced Sciences and Technology, Kobe University, Kobe, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan; Department of Bioinformatic Engineering, Osaka University, Osaka, Japan
PRIMe funding source(s)
Supported by the Japan Society for the Promotion of Science [a Grant-in-Aid for Young Scientists (B) (grant No. 18700106)].

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