DROP Met: Data Resources Of Plant Metabolomics

DROP Met, Data Resources Of Plant Metabolomics, is a repository and distribution site of the dataset obtained from our multiple MS-based metabolome analyses. Various kinds of datasets, ranging from raw fundamental data on analytical conditions to metabolic profiles of plant samples, are available to the public. We release some datasets in the raw, hoping that users in bioinformatics and metabolomics fields will develop novel algorithms and methodologies of metabolomics using our datasets. Please read Terms of Use carefully before using DROP Met.

Acknowledgement

DROP Met is maintained by DROP Met development team, which is supported in part by JST, CREST (Project name "Elucidation of Amino Acid Metabolism in Plants based on Integrated Omics Analyses").

DROP Met development team

Metabolic Systems Research Team & Integrated Genome Informatics Research Unit
RIKEN Plant Science Center

MS-DIAL demo files

Both data independent MS/MS acquisition (SWATH) and data dependent MS/MS acquisition (IDA) data sets is downloaded as the demo files of MS-DIAL. In order to use MS-DIAL program, the user has to convert the vendor's raw data to ABF file format. The demonstration for file convert can be performed via AB Sciex raw data sets (.wiff and .wiff.scan). The file converter is available at http://www.reifycs.com/english/AbfConverter/. If you want to demonstrate MS-DIAL itself, please use the converted files (.abf) from the below link. Also see MSDIAL quick start

Contents:

Japanese rice 188 cultivars LC-MS dataset

The metabolome data (NetCDF format, 188 cultivars * 4 replicates = 752 files) were obtained from 188 accessions of Japanese rice collection by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

Please cite:

  • Matsuda et al. Submitted.

Untargeted metabolome data during drought stress in Arabidopsis thaliana

The MS and MS/MS data of A. thaliana (Col-0) were acquired in positive mode of LC-QTOF-MS. The raw files were converted to netCDF and text files stored here.

Please cite:

  • Alternation of flavonoid accumulation under drought stress in Arabidopsis thaliana.
    Ryo Nakabayashi, Tetsuya Mori, Kazuki Saito
    Plant Signaling & Behavior

Contents:

Metabolome data in Oryza sativa L. cultivar Habataki and MS/MS spectra of isolated compounds from rice leaves

The MS/MS raw data were acquired in positive and negative mode of LC-QTOF-MS.

Please cite:

  • Toward better annotation in plant metabolomics: Isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses
    Zhigang Yang, Ryo Nakabayashi, Yozo Okazaki, Tetsuya Mori, Satoshi Takamatsu, Susumu Kitanaka, Jun Kikuchi, Kazuki Saito
    Metabolomics

High resolution MS/MS spectra from health-promoting crops

We collected MS/MS spectra from health-promoting crops by LC-QTOF-MS.
All data and metadata are freely available.

Contact person:

  • Ryo Nakabayashi

Acknowledgements:

  • This project was supported by Japan Advanced Plant Science Network and Strategic International Research Cooperative Program (SICP), JST.

Contents:

Development of Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO)

We chose 50 Arabidopsis mutants including a set of characterized and uncharacterized mutants, which resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry (GC-MS). All data are available for download in netCDF format.MetaboLights ID: MTBLS47.

Please cite:

  • Metabolomic Characterization of Knock-Out Mutants in Arabidopsis - Development of a Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO) Atsushi Fukushima, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa,Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi, Tomoko Narisawa, Takayuki Tohge, Manhoi Hur, Eve Syrkin Wurtele, Basil J.Nikolau, Kazuki Saito
    Plant Physiology

Metabolome data in Allium plants and MS/MS spectra of S-containing compounds

The MS raw data were acquired in the positive mode of LC-FTICR-MS.
The raw files were converted to netCDF files stored here.

Please cite:

  • Submitted.

Metabolome data in Arabidopsis mutants overaccumulating and lacking flavonoids

The MS raw data of the Arabidopsis mutants were acquired in positive mode of LC-QTOF-MS.
The raw files were converted to netCDF files stored here.

Please cite:

  • Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids
    Ryo Nakabayashi, Keiko Yonekura-Sakakibara, Kaoru Urano, Makoto Suzuki, Yutaka Yamada, Tomoko Nishizawa, Fumio Matsuda, Mikiko Kojima, Hitoshi Sakakibara, Kazuo Shinozaki, Anthony J. Michael, Takayuki Tohge, Mami Yamazaki, Kazuki Saito
    The Plant Journal

Contents:

Unstress condition
Drought stress

Metabolic profile data of RILs of G. max and G. soja

LC-ESI-QqQ-MS (UPLC-TQS, Waters) data derived from 93 Soybean RILs with excel file.

Please cite:

12C- & 13C-based metabolome data in onion bulb

The MS and MS/MS raw data were acquired in the positive mode of LC-FT-ICR-MS.
The raw files were converted to netCDF files stored here.

Please cite:

  • Combination of Liquid Chromatography-Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry with 13C labeling for Chemical Assignment of Sulfur-containing Metabolites in Onion Bulbs
    Ryo Nakabayashi, Yuji Sawada, Yutaka Yamada, Makoto Suzuki, Masami Yokota Hirai, Tetsuya Sakurai, and Kazuki Saito
    Analytical Chemistry

Metabolic profile data of LjMG RILines

Total 88 metabolites of raw LC-ESI-QqQ-MS (UPLC-TQS, Waters) data derived from 132 LjMG RILines with excel file.

Please cite:

  • "RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database" (Phytochemistry)

AtMetExpress 20 ecotypes raw LC-ESI-TOF-MS dataset

Total 200 raw LC-ESI-TOF-MS chromatogram data derived from 20 Arabidopsis accession recorded with NetCDF format. These are part of the AtMetExpress metabolite accumulation atlas. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation.

Please cite:

Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients

Aritifical biological gradients between leaft and fruit samples from tomato for broad evaluation of quantification performance.

Please cite:

  • Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients. Redestig H, Kobayashi M, Saito K, Kusano M. Anal Chem. 2011 Jun 1.

Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment

Metabolic profile data of miraculin over-expressing tomatoes grown on hydroponics (HC) and soil.

Please cite:

  • Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. Kusano, M.; Redestig, H.; Hirai, T.; Oikawa, A.; Matsuda, F.; Fukushima, A.; Arita, M.; Watanabe, S.; Yano, M.; Hiwasa-Tanas, K.; Ezura, H. & Saito, K. PLoS ONE, 2011

Contents:

Metabolite accumulation in seeds of Arabidopsis transposon-tagged mutants and accessions

Metabolic profiles in seeds of 2,656 Arabidopsis transposon-tagged mutants and 225 Arabidopsis accessions. Peak areas were measured by UPLC-ZQMS analysis for 36 metabolites and recorded with Tab Separated Variables format.

Please cite:

"Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources. Journal of Plant Research. (2010) 123, 291-298"

AtMetExpress Development raw LC-ESI-TOF-MS dataset

Total 288 raw LC-ESI-TOF-MS chromatogram data derived from 36 Arabidopsis tissues recorded with NetCDF format. These are part of the AtMetExpress metabolite accumulation atlas. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation.

Please cite:

"AtMetExpress Development: A phytochemical Atlas of Arabidopsis Develpment Plant Physiol. (2010) in press."

Mixture Dilution Series for Pre-processing Validation

Total of 27 chromatograms with replicates of three different standard mixtures. Provided for validation of the Bioconductor package TargetSearch

Please cite:

"TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics. (2009) 10:428"

Metabolic profile data of Arabidopsis four aerial tissues

Total 32 raw LC-ESI-MS chromatogram data derived from four Arabidopsis tissues (flower, rosette leaf, cauline leaf, and internode, eight replicates) recorded with NetCDF and ASCII format. Detailed information of each data files are described in the meta information (.txt) by following Metabolome Standard Initiative (MSI) recommendation. For details, please refer LC-MS branch.

Please cite:

"MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J (2009) 57,555-577"

Contents:

Widely targeted metabolomics datasets ver 1.0

We optimized multiple reaction monitoring (MRM) conditions to detect each of the 860 compounds (as of Mar 2009) by means of widely targeted metabolomics. All datasets useful to condition your measurement system are released here. ESI-MS/MS spectra are also available in ReSpect for Phytochemicals. A dataset of the metabolite accumulation patterns in 14 plants from Brassicaceae, Gramineae and Fabaceae is also released here.

Please Cite:

"Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants." Plant Cell Physiol. (2009) 50, 37-47

Comments and questions:
RIKEN Plant Science Center