SE24:/S1/M1/D1

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Sample Set Information

ID SE24
Title Combination of Liquid Chromatography−Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry with 13C‑Labeling for Chemical Assignment of Sulfur-Containing Metabolites in Onion Bulbs
Description We provide a chemical assignment strategy for S-metabolites using 12C- and 13C-based MS and tandem mass spectrometry (MS/MS) spectra recorded by Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) coupled with liquid chromatography (LC) as a case study of the metabolite of onion bulbs. We performed comprehensive peak picking using the theoretical mass difference (1.99579 Da) between 32S-containing monoisotopic ions and their 34S-substituted counterparts for 67 S-containing monoisotopic ions. From these, we identified the specific elemental composition of 22 ions. Finally, we determined that six ions were derived from S-alk(en)ylcysteine sulfoxides and glutathione derivatives.
Authors Ryo Nakabayashi, Yuji Sawada, Yutaka Yamada, Makoto Suzuki, Masami Yokota Hirai, Tetsuya Sakurai, and Kazuki Saito
Reference Nakabayashi R et al. (2013) Analytical Chemistry 85: 1310-1315
Comment The metadata is prepared by the Metabolonote administrator (Sakurai N).


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

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The web resources and information related to the species used in this study are available at Plant Genome Database Japan (PGDBj).

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Sample Information

ID S1
Title Nonlabeled onion bulbs (12-week-old)
Organism - Scientific Name Allium cepa
Organism - ID NCBI taxonomy:4679
Compound - ID
Compound - Source
Preparation Nonlabeled onion bulbs (sections) were purchased from SI Science (Japan). Onion plants were grown under 12CO2 (1.1 atom % 13C) in a growth chamber. The plants were grown for 12 weeks under controlled conditions: day/night cycle, 14/10 h; temperature, 23/15 C (day/night); relative humidity, 75%/85% (day/night); light, 600 umol/m2; and hydroponics nutrient solution, Hoagland type. After cutting 12-week-old bulbs into 1-cm squares, the samples were immediately frozen with liquid nitrogen and 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 LC-FTICR-MS, ESI Positive analysis
Method Details ID MS1
Sample Amount 20 ug dry weight
Comment The amount of the sample contained in the 1 uL liquid sample injected to the LC.

Analytical Method Details Information

ID MS1
Title LC-FTICR-MS Analysis (Positive)
Instrument LC, Agilent 1200 series (Agilent); MS, Solarix 7.0T (Bruker Daltonics)
Instrument Type LC-FTICR-MS
Ionization ESI
Ion Mode Positive
Description Extraction of Metabolites:

The freeze-dried samples were extracted with 50 uL of 80% MeOH containing 2.5 uM lidocaine per mg dry weight using a mixer mill (MM300, Retsch) with zirconia beads for 10 min at 20 Hz and 4C. After centrifugation for 10 min, the supernatant was filtered using and HLB uElution plate (Waters).


LC-FTICR-MS Analysis:

A liquid sample (1 uL) 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 um, 2.1 mm x 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.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 260000 at m/z 400); polarity, positive; calibrant, low concentration TuningMix (Agilent); lock mass target, diethylhexylphthalate (C24H38O4, [M+H]+ m/z 391.28429); MS/MS detection (resolution 35000 at m/z 400).

Comment_of_details

Data Analysis Information

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


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The mass spectrum data are available at Bio-MassBank.

Link icon database.png Link icon dropmet.png

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

Data Analysis Details Information

ID DS1
Title Data Analysis
Description Data Analysis:

The MS and MS/MS spectra were recorded using Hyster 3.0 (Bruker Daltonik GmbH), and the data were processed using DataAnalysis 4.0 (Bruker Daltonik GmbH). After noise reduction (<100000 counts), a list containing 4693 chromatographic ions was generated using the netCDF of the spectra with the appropriate software, which will be publicly available after reaching the final step. Peak picking was performed using the theoretical mass difference (1.99579 ± 0.001 Da) between 32S-monoisotopic ions and their 34S-substituted counterparts, narrowing the list to 67 S-monoisotopic ions. The elemental composition and theoretical ion patterns were calculated using SmartFormula and SmartFormula 3D with the following limiting conditions: < 1 ppm; C0-50H0-100N0-5O0-50S0-5; charge, 1.


Data Upload:

All data acquired by LC-FTICR-MS were uploaded at DROP Met in PRIMe (http://prime.psc.riken.jp/) and are freely available.

Comment_of_details
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