Useful links

Metabolome/Mass spectra/NMR spectra
AtMetExpress Development Matsuda et al. (2010) 20023150
Moto DB (Metabolome Tomato Database) Moco et al. (2006) Plant Physiol 16896233
Plantmetabolomics.org Bais et al. (2012) NAR 22080512
GMD@CSB.DB Kopka et al. (2005) Bioinformatics; Hummel et al. (2007) Metabolomics 15613389
SoyMetDB: The soybean metabolome database Joshi et al. NA
HMDB: Human Metabolome Database Wishart et al. (2009) NAR 18953024
MMMDB: Mouse Multiple Tissue Metabolome Database Sugimoto et al. (2012) NAR 22139941
YMDB: the Yeast Metabolome Database Jewison et al (2012) NAR 22064855
Metabolomics.jp Arita and Suwa (2008) BioData mining 18822113
The MetabolomeExpress Carroll et al. (2010) BMC Bioinformatics 20626915
KOMICS: Kazusa Metabolomics Portal Kazusa DNA Research Institute NA
MeltDB Neuweger et al. (2008) Bioinformatics 18765459
MetaboLights EBI
FihenLib Kind et al. (2009) Anal Chem 19928838
VocBinBase Skogerson et al. (2011) BMC Bioinformatics 21816034
SetupX Scholz and Fiehn (2007) NA
BinBase Fiehn et al. (2005) LNCS NA
NIST Stein (1999) J Am Soc Mass Spectrom NA
METLIN Smith et al. (2005) Ther Drug Monit 16404815
MMCD Cui et al. (2008) Nat Biotechnol 18259166
LMSD Sud et al. (2007) NAR 17098933
MassBank Horai et al. (2010) J Mass Spectrom 20623627
Bio-MassBank Nishioka et al. NA
ResPect Sawada et al. (2012) Phytochem 22867903
MassBase Kazusa DNA Research Institute NA
KOMIC Market Kazusa DNA Research Institute NA
BMRB Ulrich et al. (2008) NAR 17984079
SpinAssign Chikayama et al. (2010) Anal Chem 20128615

Compounds
PubChem Wang et al. (2009) NAR 19498078
ChEBI Degtyarenko et al. (2008) NAR 17932057
CAS
Chemspider Pence and Williams (2010) J Chem Educ NA
LipidMaps Fahy et al. (2007) NAR 17584797
LipidBank Watanabe et al. (2000) Glycotechnol NA
KEGG
KNApSAcK: A Comprehensive Species-Metabolite Relationship Database Afendi et al. (2012) PCP 22123792
Chemical Translation Service (CTS) Wohlgemuth et al. (2010) Bioinformatics 20829444

Enzymes/Reactions
BRENDA Chang et al. (2009) NAR 18984617
BKM-react Lang et al. (2011) BMC Biochem 21824409

Pathways
AraCyc Zhang et al. (2005) Plant Physiol 15888675
PlantCyc Plant Metabolic Network (PMN) NA
BioCyc Caspi et al. (2012) NAR 22102576
MetaCyc Caspi et al. (2012) NAR 22102576
KaPPA-View Sakurai et al. (2011) NAR 21097783
MapMan Usadel et al. (2009) PCE 19389052
AraPath Lai et al. (2012) Bioinformatics 22760305
Pathos Leader et al. (2011) Rapid Commun Mass Spectrom 22002696
UniPathway Morgat et al. (2012) NAR 22102589
SMPDB: The Small Molecule Pathway Database Frolkis et al. (2010) NAR 19948758

Tools
Metab2MeSH: annotating compounds with medical subject headings Sartor et al. (2012) Bioinformatics 22492643
MetaboSearch: Tool for Mass-Based Metabolite Identification Using Multiple Databases Zhou et al. (2012) PLoS One 22768229
MetPA Xia and Wishart (2010) Bioinformatics 20628077
Metabolite Set Enrichment Analysis (MSEA) Xia and Wishart (2010) NAR 20457745
MetaboAnalyst Xia et al. (2012) NAR 22553367
MetScape Karnovsky et al. (2012) Bioinformatics 22135418
metaP-Server: A Web-Based Metabolomics Data Analysis Tool Kastenmuller et al. (2011) J Biomed Biotechnol 20936179
CCMN and other noRMalizatioN methods for metabolomics data Redestig et al. (2009) Anal Chem 19743813
MetMask Redestig et al. (2010) BMC Bioinformatics 20426876
MS-MS Fragment Viewer Kazusa DNA Research Institute NA

Genome-scale metabolic models
AraGEM Dal'Molin et al. (2010) Plant Physiol 20044452
C4GEM Dal'Molin et al. (2010) Plant Physiol 20974891
Mintz-Oron model Mintz-Oron et al. (2012) PNAS 22184215
BioModel Database Li et al. (2010) BMC Syst Biol 20587024

Useful Web/Portal pages
TAIR Metabolome Resources Lamesch et al. (2012) NAR 22140109
PRIMe: the Platform for RIKEN Metabolomics Akiyama K. et al. (2008) In Silico Biol NA
The Metabolomics Innovation Centre
Metabolomics Software and Servers@Metabolomics Society
"Peak Alignment of LC, GC, MS, NMR data@Metabolomics Fiehn Lab"

Metabolomics society/Metabolomics communities/Metabolomics Labs
Metabolomics Society
Metabolomics Standards Initiative (MSI)
Max Planck Institute of Molecular Plant Physiology
RIKEN Plant Science Center
Dr. Kazuki Saito's Lab@Chiba Univ
IAB Keio University
IAB Metabolomics Lab (Dr. Tomoyoshi Soga)
Human Metabolome Technologies
Dr. Eiichiro Fukusaki's Lab@Osaka Univ
Dr. Hiroyuki Wariishi's Lab@Kyusyu Univ
Genaris
Kazusa Inst. Division of metabolite analysis and characterization
Metabolomics Fiehn Lab
Dr. Lloyd Sumner's Lab
Dr. Basil Nikolau's Lab
Dr. David Wishart's Lab
Dr. Roy Goodacre's Lab
Dr. Robert Hall's Lab
Dr. Matej Oresic's Lab
Dr. Warwick Dunn's Lab
Dr. Marta Cascante's Lab
Dr. Thomas Hankemeier's Lab
Dr. Mark Viant's Lab
Dr. Ute Roessner's Lab
Dr. Christoph Steinbeck's Lab
Metabolomics Australia
Dr. Dr. Lothar Willmitzer's Lab
Dr. Alisdair Fernie's Lab
Dr. Mark Stitt's Lab
Dr. Wolfram Weckwerth's Lab