SE168:/S01/M1/D01

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Sample Set Information

ID TSE1330
Title Automation of chemical assignment for identifying molecular formula of S-containing metabolites by combining metabolomics and chemoinformatics with 34S labeling
Description Introduction

Sulfur-containing metabolites (S-metabolites) in organisms including plants have unique benefits to humans. So far, few analytical methods have explored such metabolites.

Objectives
We aimed to develop an automatic chemically assigning platform by metabolomics and chemoinformatics with 34S labeling to identify the molecular formula of S-metabolites.

Results
We identified 35 molecular formulae for known S-metabolites and characterized 72 for unknown. Chemoinformatics required around 1.5 min to analyze a pair of the non-labeled and 34S-labeled data of the organ.

Conclusion
In this study, we developed an automation platform for automatically identifying the presence of S-metabolites. We identified the molecular formula of known S-metabolites, which are accessible in free databases, together with that of unknown. This analytical method did not focus on identifying the structure of S-metabolites, but on the automatic identification of their molecular formula.

Authors Nakabayashi, R., Tsugawa, H.,Mori, T. and Saito, K.
Reference Metabolomics, November 2016, 12:168, DOI: 10.1007/s11306-016-1115-5
Comment


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Sample Information

ID S01
Title Arabidopsis thaliana (ecotype Columbia-0)
Organism - Scientific Name Arabidopsis thaliana
Organism - ID NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation Arabidopsis thaliana (ecotype Columbia-0) was used in this study. Non-labeled and 34S-labeled Arabidopsis plants were prepared by SI Science CO., LTD (Saitama, Japan). The plants were individually grown in pots filled with vermiculite, which were set in a plant growth room at 25 °C under a 16 h light/8 h dark cycle for 8 weeks. A non-labeled and an 34S-labeled liquid fertilizer (Table S1) was added to the plants daily. Different parts of the flower, including the silique, leaf, stem, and root, in 8-week-old Arabidopsis plants were harvested and immediately lyophilized at −55 °C. The lyophilized materials were stored at room temperature with silica gel.
Sample Preparation Details ID
Comment

Analytical Method Information

ID M1
Title FTICR-MS (Direct infusion)
Method Details ID MS01
Sample Amount 100 μL
Comment

Analytical Method Details Information

ID MS01
Title FTICR-MS (Direct infusion)
Instrument FTICR-MS solariX 7.0 T (Bruker Daltonics)
Instrument Type
Ionization ESI
Ion Mode negative
Description Extraction of metabolites

The freeze-dried samples were extracted with 50 μL of 80 % MeOH containing 2.5 μM 10-camphorsulfonic acid, 1.25 μM reserpine, 2.5 μM ampicillin, and 2.5 μM CHAPS as internal standards for calibration per mg dry weight using a mixer mill (MM300, Retsch) with zirconia beads for 7 min at 18 Hz and 4 °C. After 10 min of centrifugation, the supernatant was filtered with an HLB μElution plate (Waters). Extracts were routinely diluted with 80 % MeOH at a ratio of 1:1000 (extract: 80 % MeOH).

Direct infusion analysis
Ultra-high-resolution metabolome data were acquired using an FTICR-MS solariX 7.0 T (Bruker Daltonics) with an ESI source. The following settings were applied: MS Detection; Acquisition Mass Control (mass range, m/z 100–800; estimated resolution power, 530,000 at m/z 400; transient length, 3.9147 s); Data Storage (save full profile spectrum, on; save FID file, on); Accumulation (scan time, 100; source accumulation, 0.01 s; ion accumulation time, 0.1 s; ion cooling time, 0 s; time of flight, 0.45 s); API Source (source type, ESI; capillary, 4500 V; end plate offset, 1000 V); Source Gas Tune (nebulizer 1.0 bar; dry gas, 2.0 L/min; dry temperature, 200 °C); Source Optics (capillary exit, −220 V; deflector plate, −200 V; funnel 1, −150 V; skimmer 1, −25 V; funnel RF amplitude, 180 Vpp); Octopole (frequency, 5 MHz; RF amplitude, 350 Vpp); Collision Cell (collision voltage, 0.8 V; DC extract bias, −0.9 V; RF frequency, 2 MHz; collision RF amplitude, 850 Vpp); Transfer Optics (time of flight, 0.45 ms; frequency, 6 MHz; RF amplitude, 400 Vpp); Infinity Cell (transient exit lens, 20 V; analyzer entrance, 10 V; side kick, 0 V; side kick offset, 1.5 V; front trap plate, −0.5 V; back trap plate, −0.5 V; sweep excitation power, 20 %); Multiple Cell Accumulations (number of ICR cell fills, 1); Gated Trapping (gated trapping mode, off); Polarity, negative. MS spectra were internally calibrated using the MS spectra of internal standards.

Comment_of_details

Data Analysis Information

ID D01
Title Data analysis
Data Analysis Details ID DS1
Recommended decimal places of m/z
Comment


Data Analysis Details Information

ID DS1
Title Data analysis
Description The MS spectra were recorded using Hystar 4.0 (Bruker Daltonik GmbH, Bremen, Germany) and the data were processed using DataAnalysis 4.2 (Bruker Daltonik GmbH). Internal calibration was performed using the exact mass of the internal standards. Molecular formulae were determined from an in-house database storing metabolite information downloaded on April 1, 2015, from metabolome databases: [(BMDB (http://www.cowmetdb.ca/cgi-bin/browse.cgi) (2697), ChEBI (Hastings et al. 2013) (14,546), DrugBank (Wishart et al. 2006) (5355), ECMDB (Guo et al. 2013) (987), FooDB (http://foodb.ca/) (6441), HMDB (Wishart et al. 2007) (9652), KNApSAcK (Afendi et al. 2012) (13,825), PlantCyc (http://www.plantcyc.org/) (2421), PubChem Classification Browser (Biosystems and Pathways, https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72) (8242), SMPDB (Frolkis et al. 2010) (1187), T3DB (Lim et al. 2010) (1726), UNPD (http://pkuxxj.pku.edu.cn/UNPD/) (32,952), and YMDB (Jewison et al. 2012) (1047)]. The number of molecular formulae downloaded from each database is shown in the parentheses. A personal computer (Windows 10 Intel Xeon (R) CPU E5-2650 v3 (2.3 GHz) with 128 GB RAM) required around 1.5 min to analyze a pair of the non-labeled and 34S-labeled data of a certain organ. The program named SMetSearch can be freely downloaded from the standalone software section of the RIKEN PRIMe database (http://prime.psc.riken.jp/Metabolomics_Software/SmetSearch/index.html).
Comment_of_details
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