ONTOLOGY SOURCE REFERENCE
Term Source Name	NCBITAXON	OBI	BAO	BTO	MS	CHMO	VIVO	MESH	EFO
Term Source File	http://data.bioontology.org/ontologies/NCBITAXON	http://data.bioontology.org/ontologies/OBI	http://data.bioontology.org/ontologies/BAO	http://data.bioontology.org/ontologies/BTO	http://data.bioontology.org/ontologies/MS	http://data.bioontology.org/ontologies/CHMO	http://data.bioontology.org/ontologies/VIVO	http://data.bioontology.org/ontologies/MESH	http://data.bioontology.org/ontologies/EFO
Term Source Version	2	22	19	22	86	18	2	6	113
Term Source Description	National Center for Biotechnology Information (NCBI) Organismal Classification	Ontology for Biomedical Investigations	BioAssay Ontology	BRENDA Tissue and Enzyme Source Ontology	Mass Spectrometry Ontology	Chemical Methods Ontology	VIVO Ontology for Researcher Discovery	Medical Subject Headings	Experimental Factor Ontology
INVESTIGATION
Investigation Identifier	MTBLS528
Investigation Title	Investigation
Investigation Description
Investigation Submission Date	2017-08-21
Investigation Public Release Date	2018-04-03
Comment[Created With Configuration]	C:UsersMDesktopISAcreatorMetaboLightsConfigurationsMetaboLightsConfig20150707
Comment[Last Opened With Configuration]	MetaboLightsConfig20150707
INVESTIGATION PUBLICATIONS
Investigation PubMed ID
Investigation Publication DOI
Investigation Publication Author List
Investigation Publication Title
Investigation Publication Status
Investigation Publication Status Term Accession Number
Investigation Publication Status Term Source REF
INVESTIGATION CONTACTS
Investigation Person Last Name
Investigation Person First Name
Investigation Person Mid Initials
Investigation Person Email
Investigation Person Phone
Investigation Person Fax
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Investigation Person Roles Term Source REF
STUDY
Study Identifier	MTBLS528
Study Title	The natural variance of the Arabidopsis floral secondary metabolites
Study Description	Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as transcripts, proteins and growth and flowering related phenotypes.
Study Submission Date	2017-08-21
Study Public Release Date	2018-04-03
Study File Name	s_MTBLS528.txt
Comment[License]	EMBL-EBI Terms of Use
Comment[Revision]	2
Comment[Revision Date]	2025-09-04
Comment[Revision Log]	updating data license
STUDY DESIGN DESCRIPTORS
Study Design Type	untargeted metabolites	Secondary Metabolism	plant	high-performance liquid chromatography-mass spectrometry
Study Design Type Term Accession Number		http://purl.bioontology.org/ontology/MESH/D064210	http://www.bioassayontology.org/bao#BAO_0000605	http://purl.obolibrary.org/obo/CHMO_0000796
Study Design Type Term Source REF		MESH	BAO	CHMO
STUDY PUBLICATIONS
Study PubMed ID	29611844
Study Publication DOI	10.1038/sdata.2018.51
Study Publication Author List	Takayuki Tohge, Monica Borghi, Alisdair R. Fernie.
Study Publication Title	The natural variance of the Arabidopsis floral secondary metabolites
Study Publication Status	Published
Study Publication Status Term Accession Number
Study Publication Status Term Source REF
STUDY FACTORS
Study Factor Name	genotype	replicate
Study Factor Type	genotype	replicate
Study Factor Type Term Accession Number	http://www.ebi.ac.uk/efo/EFO_0000513	http://www.ebi.ac.uk/efo/EFO_0000683
Study Factor Type Term Source REF	EFO	EFO
STUDY ASSAYS
Study Assay File Name	a_MTBLS528_metabolite_profiling_mass_spectrometry.txt
Study Assay Measurement Type	metabolite profiling
Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000366
Study Assay Measurement Type Term Source REF	OBI
Study Assay Technology Type	mass spectrometry
Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000470
Study Assay Technology Type Term Source REF	OBI
Study Assay Technology Platform	LTQ XL (Thermo Scientific)
STUDY PROTOCOLS
Study Protocol Name	Sample collection	Extraction	Chromatography	Mass spectrometry	Data transformation	Metabolite identification
Study Protocol Type	Sample collection	Extraction	Chromatography	Mass spectrometry	Data transformation	Metabolite identification
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Study Protocol Description	Seeds of Arabidopsis natural accessions (Table 1) were germinated on 1/2 MS salts solidified with 1% of agar. 14 days after planting, the seedlings were transferred onto soil (GS-90 Einheitserde; Gebrueder Patzer) and grown under standard greenhouse conditions until flowering (photoperiod 16-8 hr, light-dark; temperature 20-16 °C). Fully open mature flowers were harvested and immediately frozen in liquid nitrogen for further analysis.	Flower tissues were ground with liquid nitrogen and homogenized in a mixer mill for 3 min at 25 Hz with a zirconia bead and 20 µl of extraction buffer (80% methanol, prepared with 5 µg/ml isovitexin as an internal standard) per mg of ground tissue. Thereafter, the supernatant was separated from the cellular debris via centrifugation at 12,000 x g.	Samples were run on a Surveyor HPLC system (Thermo, USA), 150 x 2 mm, 2.0 µm particle, HPLC column at 28 °C oven temperature. The solvents used for the assay consisted of water containing 0.1% v/v formic acid (Solvent A) and an acetonitrile solution containing 0.1% v/v formic acid (Solvent B). Gradient [time (min)/%B] starting: 2.0/0, 4.0/15, 14.0/32, 19.0/50, 19.01/100, 21.0/100, 21.01/0, 23.0/0 at flow rate 0.20 ml/min. Injection volume was 2 µl.	The compounds were detected using a Thermo LTQ mass spectrometer with electrospray ionization (ESI) mode in positive and negative ion detection mode with a scan range from 100–2000 m/z. The LTQ-XP used the Xcalibur software (Thermo Finnigan, USA) version 2.1.0 for data acquisition.	Data was not transformed to any other format.	Data were processed using Xcalibur 2.1.0 software, and peak identification and annotation implemented through a combination of the following approaches: standard chemical confirmation, MS/MS and retention time profiling, mutant analysis, literature/database survey.
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Study Protocol Parameters Name		Post Extraction;Derivatization	Chromatography Instrument;Column type;Column model	Scan polarity;Scan m/z range;Instrument;Mass analyzer;Ion source
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Study Protocol Parameters Name Term Source REF		;	;;	;;;;
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STUDY CONTACTS
Study Person Last Name	Takayuki
Study Person First Name	Tohge
Study Person Mid Initials
Study Person Email	tohge@bs.naist.jp
Study Person Phone	81-743-72-5480
Study Person Fax
Study Person Address	Nara, Ikoma, Japan
Study Person Affiliation	NAIST
Study Person Roles	Principal Investigator Role
Study Person Roles Term Accession Number	http://vivoweb.org/ontology/core#PrincipalInvestigatorRole
Study Person Roles Term Source REF	VIVO
