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Sample Set Information

Title LC-MS analysis of 15 vegetables and fruits
Description This study is aimed to a comprehensive annotation of metabolites in major vegetables and fruits produced in Japan.
Authors Sakurai N 1, Suda K 1, and Takahashi S 2 (1 Kazusa DNA Research Institute, 2 KAGOME CO. LTD.)
Reference Akimoto N, Ara T, Nakajima D, Suda K, Ikeda C, Takahashi S, Muneto R, Yamada M, Suzuki H, Shibata D, Sakurai N (2017) FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry. Scientific Reports 7: 1243

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Sample Information

ID S05
Title Chinese cabbage (shoot)
Organism - Scientific Name Brassica rapa var. pekinensis
Organism - ID NCBI taxonomy:3711
Compound - ID
Compound - Source
Sample Preparation Details ID SS1

Sample Preparation Details Information

Title Purchased in a local market
Description Plant samples were prepared from materials purchased at a local market in Tochigi prefecture, Japan. The parts of plant materials were prepared from three individual materials sold, freeze-dried, ground to powder in mortar and pestle, mixed three preparations, and stored at -80 ºC until use.

Analytical Method Information

Title Method 5: ESI Positive, Data dependent MS2/MS3 scan (FT, IT, IT)
Method Details ID MS5
Sample Amount 0.5 mg / 20 ul injected
Comment [MassBase ID] MDLC1_47230

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The raw (binary) and near-raw (text) files of this analysis are available at MassBase.

Analytical Method Details Information

Title LC-FT-MS, ESI, Positive (method 5)
Instrument Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)
Instrument Type LC-FTICR-MS
Ionization ESI
Ion Mode Positive
Description Freeze-dried powder of plant material was extracted with 75% methanol containing 25 µM of 7-hydroxy-5-methylflavone as an internal standard. After homogenization using a Mixer Mill MM 300 (Quiagen) at 25 Hz for 2 min twice, homogenates were centrifuged (17,400 g, 5 min, 4 ºC). The supernatant was filtered through 0.2 µm PTFE membrane (Millipore). Hydrophobic compounds in the filtrate were removed by absorbing to C18 silica column (MonoSpin C18, GL Science, Tokyo, Japan).

20 µl of methanol solution was applied to a TSK-gel column ODS-100V (4.6 x 250 mm, 5 µm; TOSOH). Water (HPLC grade; solvent A) and acetonitrile (HPLC grade; solvent B) were used as the mobile phase with 0.1% v/v formic acid added to both solvents. The gradient program was as follows: 3% B (0 min), 97% B (90 min), 97% B (100 min), 3% B (100.1), and 3% B (107 min). The flow rate was set to 0.25 ml/min (0-100 min) and 0.5 ml/min (100.1-107 min). The flow rate was set to 0.5 ml/min, and the column oven temperature was set at 40 ºC. Compounds are detected in ESI-positive mode in the range m/z 100-1500. Multistage MSn analyses were carried out using collision induced dissociation (CID) in a linear ion trap detector at a normalized collision energy of 35.0% and an isolation width of 4.0 (m/z), and monitored by both ion trap detector and FT-ICR detector at 25,000 (at m/z 400) mass resolution. The ESI setting was as follows: spray voltage 4.0 kV and capillary temperature 300 ºC. Nitrogen sheath gas and auxiliary gas were set at 40 and 15 arbitrary units, respectively. To monitor HPLC elution, a photodiode array detector was used in the wavelength range 200–650 nm.

Mass scan events were set as follows (referred as method 5): full mass scan with FT-ICR in resolution 12,500, MS2 scans for the most intense 5 ions of full mass scan with IT, and MS3 scans for the most 2 ions of MS2 scan with IT. A dynamic exclusion setting was applied as follows: repeat count, 3; repeat duration, 30 sec; exclusion list size, 500; margin, 10 ppm, and exclusion duration, 20.

The data were acquired by Xcalibur software version 2.07 (Thermo Fisher Scientific).


Data Analysis Information

Title Peak detection using PowerGet and FlavonoidSearch analysis
Data Analysis Details ID DS1
Recommended decimal places of m/z default

Data Analysis Details Information

Title For auto-annotation by FlavonoidSearch
Description The raw data generated by Xcalibur software were converted to mzXML format using MSConvert function of ProteoWizard software ver.3.0.6447. Metabolite peaks were detected by PowerGet software which is slightly modified from the original to enable batch processing.

The MS2 and MS3 spectra obtained within the full width at half maximum height of the peaks that eluted in a range from 15 to 90 min and annotated as protonated adduct were extracted from the mzXML file using an in-house Java program and used for FlavonoidSearch Tool (FsTool) ver.0.1.10. Tool (FsTool) ver.0.1.10. The mass tolerances of FsTool for precursor ion detected in IT-MS2 scan and fragment ions in IT-MS3 scan were set to 0.2 Da and 0.2 Da, respectively.

The MS3 spectra were searched by FlavonoidSearch tool (FsTool) and the results of the peaks with the Jaccard score > 0.3 were exported to text files in TogoMD format.

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