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.
MeKO: 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

Sakurai et al. (2013) PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation. Plant Cell Physiol. 54:e5 [PubMed]
Akiyama et al. (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 8, 0027. </isb/2008/08/0027/> [PubMed]

Modified: 2012-10-31

Comments and questions:
RIKEN Plant Science Center