SE52:/S01/M01

From Metabolonote
jump-to-nav Jump to: navigation, search

Sample Set Information

ID SE52
Title Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity
Description A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals.The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.
Authors Fumio Matsuda, Ryo Nakabayashi, Yuji Sawada, Makoto Suzuki, Masami Yokota Hirai, Shigehiko Kanaya, Kazuki Saito
Reference Matsuda F et al. (2011) Front. Plant Sci. 2:40. doi: 10.3389/fpls.2011.00040
Comment


Link icon article.png

Link icon database.png Link icon dropmet.png

The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

ID S01
Title Seeds of 20 accessions of Arabidopsis thaliana
Organism - Scientific Name Arabidopsis thaliana
Organism - ID NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation Seeds of 20 accessions of Arabidopsis thaliana, CS22676 Bay-0, CS22677 Bor-4, CS22678 Br-0, CS22679 Bur-0, CS22680 C24, CS22681 Col-0, CS22682 Cvi-0, CS22683 Est-1, CS22684 Fei-0, CS22685 Goettingen-7, CS22686 Ler-1, CS22687 NFA-8, CS22688 RRS-7, CS22689 RRS-10, CS22690 Sha, CS22691 Tamm-2, CS22692 Ts-1, CS22693 Tsu-1, CS22694 Van-0, and CS22695 Lov-5, were obtained from the ABRC.
Sample Preparation Details ID SS01
Comment

Sample Preparation Details Information

ID SS01
Title Sample Preparation
Description The seeds were soaked on MS agar plates and then incubated at 22°C under 16 h day and 8 h night conditions. At 18 days after germination, the aerial parts of the seedlings were harvested.
Comment_of_details

Analytical Method Information

ID M01
Title Metabolic profiling analysis using LC-ESI-Q-Tof/MS
Method Details ID MS01
Sample Amount 3μl
Comment


Analytical Method Details Information

ID MS01
Title Metabolic profiling analysis using LC-ESI-Q-Tof/MS
Instrument Waters Acquity UPLC system and Waters Q-Tof Premier
Instrument Type UPLC-QTOF-MS
Ionization ESI
Ion Mode Negative
Description The collected sample tissues were weighed and stored at −80°C until analysis. The frozen tissues of independent plants were homogenized in five volumes of 80% aqueous methanol containing 0.1% acetic acid, 0.5 mg/l of lidocaine, and d-camphor sulfonic acid (Tokyo Kasei, Tokyo, Japan) using a mixer mill (MM 300, Retsch) with a zirconia bead for 6 min at 20 Hz. Next, the samples were centrifuged at 15,000 g for 10 min and filtered (Ultrafree-MC filter, 0.2 μm; Millipore, Bedford, MA, USA). The sample extracts were then applied to an HLB μElution plate (Waters, Milford, MA, USA) that had been equilibrated with 80% aqueous methanol containing 0.1% acetic acid.

The eluates (3 μl) were subsequently subjected to metabolome analysis by LC coupled with electrospray quadrupole time-of-flight tandem MS using an Acquity BEH ODS column (LC-ESI-Q-Tof/MS, HPLC: Waters Acquity UPLC system; MS: Waters Q-Tof Premier). The metabolome analysis and data processing were conducted according to a previously described method (Matsuda et al., 2009c, 2010a). Briefly, the metabolome data were obtained in the negative ion mode (m/z 100–2,000; dwell time: 0.45 s; interscan delay: 0.05 s, centroid), from which a data matrix was generated with the aid of MetAlign (De Vos et al., 2007; Lommen, 2009). In order to reduce a redundancy of the data matrix, fragment ions were removed by a following procedure. A metabolite signal was removed from the matrix when there is another intense peak eluted at similar retention times [within the retention time threshold (<0.5 s)] with the highest correlation coefficient above the threshold value (>0.8). The analysis was conducted using five biological replicates of 20 accessions, from which a data matrix composed of 703 signals (peaks) was obtained (Table S1 in Supplementary Material). The number of signals would not reflect an exact number of detected metabolites due to the complex nature of the metabolome data.

To construct MS2T libraries, the extracts of five ecotypes were mixed and utilized for the MS2T data acquisition. The analyses were repeatedly conducted for four mixtures by previously described methods (Matsuda et al., 2009c). Each MS2T entry was assigned a unique accession code, such as ATH10n03690, in which ATH10n is the name of the library and 03690 is the entry number. All data obtained in this study are available at the PRIMe website1 (Akiyama et al., 2008).

Comment_of_details


Link icon database.png Link icon ms2t.png

The peak data files of this analysis are available at MS2T.

Personal tools
View and Edit Metadata
Variants
Views
Actions