SE130:/S1/M1/D1

Sample Set Information

ID	TSE14
Title	Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography−Fourier Transform Ion Cyclotron Resonance−Mass Spectrometry
Description	BACKGROUND: The chemical assignment of metabolites is crucial to understanding the relation between food composition and biological activity. OBJECTIVE: This study was designed to detect and chemically assign sulfur-containing metabolites by using LC-Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) in Allium plants. METHODS: Ultrahigh resolution (>250,000 full width at half-maximum) and mass accuracy (<1 mDa) by FTICR-MS allowed us to distinguish ions containing sulfur isotopes ((32)S and (34)S). RESULTS: Putative 69 S-containing monoisotopic ions (S-ions) were extracted from the metabolome data of onion (Allium cepa), green onion (Allium fistulosum), and garlic (Allium sativum) on the basis of theoretical mass differences between (32)S-ions and their (34)S-substituted counterparts and on the natural abundance of (34)S. Eight S-ions were chemically assigned by using the reference data according to the guidelines of the Metabolomics Standards Initiative. Three ions detected in garlic were assigned as derived from the isomers γ-glutamyl-S-1-propenylcysteine and γ-glutamyl-S-2-propenylcysteine and as S-2-propenylmercaptoglutathione on the basis of differences in key product ions identified in reference tandem MS spectra. CONCLUSION: The ability to discriminate between such geometric isomers will be extremely useful for the chemical assignment of unknown metabolites in MS-based metabolomics.
Authors	Ryo Nakabayashi, Yuji Sawada, Morihiro Aoyagi, Yutaka Yamada, Masami Yokota Hirai, Tetsuya Sakurai, Takahiro Kamoi, Daryl D Rowan, Kazuki Saito
Reference	Nakabayashi et al. (2016) The Journal of Nutrition.13:397S–402S doi: 10.3945/jn.114.202317.
Comment	The raw files were converted to netCDF files and stored in DROP Met as "Metabolome data in Allium plants and MS/MS spectra of S-containing compounds"

PubMed

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

Sample Information

ID	S1
Title	Red Onion
Organism - Scientific Name	Allium cepa L.
Organism - ID	NCBI taxonomy 4679
Compound - ID
Compound - Source
Preparation	Edible onions, green onions, and garlic were purchased in a supermarket in Tokyo, Japan. The samples were immediately frozen, lyophilized, and ground. Materials were stored at room temperature with silica gel until use.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M1
Title	LC-FTICR-MS
Method Details ID	MS1
Sample Amount	1 μL
Comment

Analytical Method Details Information

ID	MS1
Title	LC-FTICR-MS analysis
Instrument	LC, Agilent 1200 series; MS, Bruker Daltonics solariX 7.0 T
Instrument Type	LC-FTICR-MS
Ionization	ESI
Ion Mode	Positive
Description	Extraction of metabolites The freeze-dried samples were extracted with 50 μL of 80% MeOH containing 2.5 μM lidocaine per mg dry weight using a mixer mill (MM300, Retsch) with zirconia beads for 10 min at 20 Hz and 4 °C. After centrifugation for 10 min, the supernatant was filtered using an HLB μElution plate (Waters). LC–FTICR-MS Analysis A liquid sample (1 μL) was analyzed using LC–FTICR-MS (LC, Agilent 1200 series; MS, Bruker Daltonics solariX 7.0 T). Analytical conditions were as follows. LC: column, Xselect CSH C18 (3.5 μm, 2.1 mm ×150 mm, Waters); solvent system, solvent A (water with 0.1% formic acid) and solvent B (acetonitrile with 0.1% formic acid); gradient program, 99.5% A/0.5% B at 0 min, 0.5% A/99.5% B at 30.0 min, 0.5% A/99.5% B at 45.0 min, 99.5% A/0.5% B at 45.1 min, and 99.5% A/0.5% B at 60.0 min; flow rate, 0.3 mL/min; column temperature, 35 °C; wavelength, 200–600 nm; MS detection (resolution 260 000 at m/z 400, see Figure S1 in the Supporting Information); polarity, positive; calibrant, low concentration TuningMix (Agilent); lock mass target, diethylhexylphthalate (C24H38O4, [M + H]+m/z 391.28429); MS/MS detection (resolution 35 000 at m/z 400, see Figure S2 in the Supporting Information).
Comment_of_details	Nakabayashi et al. Anal Chem. 2013 Feb 5;85(3):1310-5.

PubMed

Data Analysis Information

ID	D1
Title	MS and MS/MS
Data Analysis Details ID	DS1
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS1
Title	Data analysis
Description	MS and MS/MS spectra were recorded by using Hystar 3.0 software (Bruker Daltonik). Data were processed by using DataAnalysis 4.0 (Bruker Daltonik). The raw files were converted to netCDF (named HIFI_004 for A. sativum, 006 for A. fistulosum, and 008 for A. cepa). Peak selection was performed by using the theoretical mass difference (1.99579 ± 0.001 Da) between 32S-monoisotopic ions and their 34S-substituted counterparts and natural abundance of 34S (4.29 ± 5%). S-ions were extracted under the following conditions: mass tolerance, <1 mDa; retention time, 1–15 min. Signal intensity values of all ions were divided by the signal intensity value of the internal standard lidocaine for normalization. To obtain S-ions with redundant signal intensity, ions with an intensity <0.1 were eliminated. Peak alignment was conducted by using Progenesis CoMet (Nonlinear Dynamics). The software MeV 4.8 (http://www.tm4.org/mev.html) was used for hierarchical cluster analysis. Pearson's correlation analysis was used in this analysis. The elemental composition was calculated by using SmartFormula (Bruker Daltonik) with the following limiting conditions: <1 ppm; C0−50H0−100N0−5O0−50S0−5; charge, 1.
Comment_of_details