SE61:/S21/M015/D1

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	S21
Title	Shoot of cultivation shelf grown parsley
Organism - Scientific Name	Petroselinum crispum, Paramount
Organism - ID	NCBI taxonomy:4043
Compound - ID
Compound - Source
Preparation	Hydroponically grown in a cultivation shelf. Shoot was harvested.
Sample Preparation Details ID	SS2
Comment

Sample Preparation Details Information

ID	SS2
Title	Cultivation in a cultivation shelf
Description	The parsley seeds (Kaneko Seeds Co. LTD., KS100-542, Gunma, Japan) were germinated on a watered filter paper (Whatman 1002-150, GE Healthcare Japan) in a petri dish, and seedlings were grown 14 days in a cultivation shelf under fluorescent lamps (Biolux-A, NEC Corp., Tokyo, Japan) in 16 hr light / 8 hr dark regime at 25 ºC. The seedlings were transplanted on vermiculite (10865595 SK Agri K.K., Gunma, Japan), and grown 164 days under the same condition fertilizing with a culture medium containing 3 mM KNO3, 1 mM Ca(NO3)2, 0.5 mM MgSO4, 0.5 mM NH4H2PO4, 50 µM Fe-EDTA, 49 µM H3BO3, 9 µM MnSO4, 0.8 µM ZnSO4, 0.3 µM CuSO4, and 0.1 µM Na2MoO4. Shoot was harvested, ground to powder in liquid nitrogen by mortar and pestle, and stored at -80 ºC until use.
Comment_of_details

Analytical Method Information

ID	M015
Title	Method 5: ESI Positive, Data dependent MS2/MS3 scan (FT, IT, IT)
Method Details ID	MS5
Sample Amount	5 mg / 20 ul injected
Comment	Extractions were triplicated from the same sample and equal volume of the extracts were added and analyzed. [MassBase ID] MDLC1_47225

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

Analytical Method Details Information

ID	MS5
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	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). 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 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).
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

Data Analysis Information

ID	D1
Title	PowerGetBatch, FlavonoidSearch
Data Analysis Details ID	DS2
Recommended decimal places of m/z	default
Comment	The data from S02_M01, S02_M02 and S02_M03 were used as mock data. The data from S21_M015 were used for extraction of MSn spectra.

Data Analysis Details Information

ID	DS2
Title	PowerGetBatch 2: manual curation, MSn from raw, FlavonoidSearch
Description	The raw data generated by Xcalibur software was 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 (PowerGetBatch). False positive peaks detected from background noise signals and peaks detected the mock samples were removed manually. 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 proton adduct were extracted from the mzXML file using an in-house Java program. The MS2 and MS3 spectra were used for flavonoid annotation using FlavonoidSearch Tool (FsTool) ver.0.1.10. The mass tolerances of FsTool for precursor ion detected in FT-full scan, IT-MS2 scan, and fragment ions in IT-MSn scan were set to 0.01 Da, 0.2 Da, and 0.2 Da, respectively. The results of the peaks with the Jaccard score > 0.3 in the FlavonoidSearch were exported to text files in TogoMD format.
Comment_of_details