Platform for RIKEN Metabolomics

About PRIMe

PRIMe, the Platform for RIKEN Metabolomics, is a Web-based service for metabolomics and transcriptomics as systems for understanding life. This project measures standard metabolites by means of multi-dimensional NMR spectroscopy, GC/MS, LC/MS, and CE/MS. We also provide unique tools for metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.

Sections

What's New?

2014-10-08
The directory [Targeted and Non-targeted analysis software] was moved to newly opened [Standalone software] section.
2014-06-19
[DROP Met] Data was added.
2014-01-24
[MetBoard] Newly opened.
2013-09-26
[DROP Met] Data was added.
2013-07-01
[DROP Met] Data was added.
2013-06-20
[HIFI] Newly opened.
2013-04-25
[DROP Met] Data was added.
2013-04-01
[Targeted and Non-targeted analysis software] Newly opened.
2013-02-15
[DROP Met] Data was added.
2013-02-13
[DROP Met] Data was added.
2012-10-31
[PRIMeLink] Newly opened.
2012-09-14
[SpinAssign] Added more than 510 NMR spectra for Methanol/HEPES extracted samples.
2012-08-10
[MeKO] Newly opened.
2011-08-10
[AtMetExpress] New content available.
2010-09-10
[ReSpect] Newly opened.
2009-04-07
[MS2T] Newly opened.
2008-06-26
[Standard spectrum search] Dramatically changed standard data, ex. 300% increase of NMR data, and version up of "current status" metabolic map.
[SpinAssign] Modified example input data to experimental plant extract, measured by our laboratory. Searching total of more than 500 of 13C-HSQC cross peaks with our new NMR data base.
2006-12-29
[SpinAssign] Released a stable service.
[Standard Spectrum Search] Released a stable service.
[Cluster Cutting] Changed the service name.
[Correlated Gene Search] Changed the service name.
2006-08-30
[Site Map] Added a page.
[Cluster Extract] Updated "Using Cluster Extract"
[Cluster Extract] Revised the cutting program.
[Coexpression Gene Search] Released a stable service.
[Coexpression Gene Search] Updated "Using Coexpression Gene Search"
2006-08-17
[Coexpression Gene Search] Added a Biolayout-compatible output format and revised the Pajek-compatible output format.

Web Applications

Standard Spectrum Search
A database of the standardized spectra of a range of compounds based on NMR chemical shifts and on GC and LC mass spectrometer.
MS/MS spectral tag (MS2T) viewer
MS/MS spectral libraries of plant secondary metabolites created for LC-MS metabolomics.
ReSpect for Phytochemicals
A collection of literature and in-house MSn spectra data for the plant metabolomics research.
PRIMeLink
Innovative integration of the databases in PRIMe and bi-directionalsearchable function from the gene or metabolite perspective.
HIFI
Heteroatom-containing Ion Finder (HIFI) is a tool for Liquid chromatography Fourier transfer ion cyclotron resonance-mass spectrometry.
mekoMeKO
Metabolomic characterization of 50 Arabidopsis mutants and the database as a functional genomics tool.
SpinAssign
A large-scale annotation of detection of metabolites by NMR from user 13C-HSQC peaks.
Correlated Gene Search
A search tool for finding correlated gene pairs in the AtGenExpress data, with conversion to network-viewer software format.
Cluster Cutting
A tool for cutting our AtGenExpress hierarchical clustering data.

Distibution and Redistribution

MetBoard
MetBoard provides information of standard compounds which can be divided from providers for collaboration work.
DROP Met
Contains various datasets obtained from mass spectrometer-based metabolome analyses
Standalone software
Contains MS-DIAL, MRMPROBS, MRM-DIFF, AIoutput, and Excel Macro applications. Newly developed software will be updated here.
KNApSAcK
A comprehensive species-metabolite relationships database
Simple BL-SOM
An application for creating a batch-learning self-organizing map

Publications

Modified: 2012-10-31

Comments and questions:
RIKEN Plant Science Center