SE61:/S01/M03

Sample Set Information

ID	SE61
Title	LC-MS analysis of parsley
Description	Comprehensive analysis of metabolites in parsley (Petroselium crispum, Paramount) was performed by several combination of sample preparation and analytical conditions. Parsley was hydroponically grown in a greenhouse (S11-S13) or a cultivation shelf (S21-S26) using control medium and stable isotope (15N or 34S)-containing medium.
Authors	Sakurai N, Suda K (Kazusa DNA Research Insitute)
Reference	Akimoto N, Ara T, Nakajima D, Suda K, Ikeda C, Takahashi S, Muneto R, Yamada M, Suzuki H, Shibata D and Sakurai N (2017) FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry. Scientific Reports 7: 1243
Comment

A part of data is used in this article.

Sample Information

ID	S01
Title	Mock for greenhouse grown parsley
Organism - Scientific Name
Organism - ID
Compound - ID
Compound - Source
Preparation	The same procedure of metabolite extraction and analysis were performed without parsley materials.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M03
Title	ESI Positive, Method1, Replication 3
Method Details ID	MS1
Sample Amount	20 ul injected
Comment	An independent preparation of the mock sample was performed for this instrumental analysis. [MassBase ID] MDLC1_47218

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

Analytical Method Details Information

ID	MS1
Title	LC-FT-MS, ESI, Positive (method 1)
Instrument	Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)
Instrument Type	LC-FTICR-MS
Ionization	ESI
Ion Mode	Positive
Description	Frozen powder of plant material was extracted with three times volumes of 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). Mock sample was prepared with the same procedure without adding the plant material. 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 min), 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 1): full mass scan with FT-ICR in resolution 100,000 and MS2 scans for the most intense 5 ions of full mass scan with ion trap (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).
Comment_of_details	[column] TSK-gel ODS-100V (4.6 x 250 mm, 5 micrometer; TOSOH) [gradient] Solvent A: water containing 0.1% v/v formic acid; Solvent B: acetonitrile containing 0.1% v/v formic acid; Gradient: 3% B (0 min), 97% B (90 min), 97% B (100 min), 3% B (100.1 min), and 3% B (107 min) [total separation time] 107 min