Sample Set Information
|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|
|Title||Shoot of greenhouse grown parsley|
|Organism - Scientific Name||Petroselinum crispum, Paramount|
|Organism - ID||NCBI taxonomy:4043|
|Compound - ID|
|Compound - Source|
|Preparation||Hydroponically grown in a greenhouse. Shoot was harvested.|
|Sample Preparation Details ID||SS1|
Sample Preparation Details Information
|Title||Cultivation in a greenhouse|
|Description||The parsley seeds (Kaneko Seeds, Co. LTD. KS100-542, Gunma, Japan) were germinated on watered sand. The 20 days-old seedlings were transplanted on baked foamed clay pebbles (Hydroball, Toshi Engei Col. LTD, Saitama, Japan) in a green house, and grown 63 days with 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.|
Analytical Method Information
|Title||Method 4: ESI Positive, Data dependent MS2 scan (FT, IT)|
|Method Details ID||MS4|
|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_47222
Analytical Method Details Information
|Title||LC-FT-MS, ESI, Positive (method 4)|
|Instrument||Agilent1100 HPLC (Agilent), LTQ-FT (Thermo Fisher Scientific)|
|Description|| Frozen powder of plant material was extracted with three times volumes of methanol containing 25 uM 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 degree celsius). The supernatant was filtered through 0.2 um 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 ul of methanol solution was applied to a TSK-gel column ODS-100V (4.6 x 250 mm, 5 um; 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 degree celsius. 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 degree celsius. 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 to as method 4): 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 not applied.
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
|Title||Peak detection using PowerGet|
|Data Analysis Details ID||DS1|
|Recommended decimal places of m/z||default|
|Comment||The data from S01_M01, S01_M02 and S01_M03 were used as mock sample data. The data from S11_M014, S11_M015 and S11_M016 were used for extraction of MSn spectra.|
Data Analysis Details Information
|Title||PowerGetBatch 1: manual curation, MSn from raw|
|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 (PowerGetBatch).
False positive peaks extracted from background noise signals and peaks detected in the mock samples were manually removed. 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 results were exported to text files in TogoMD format.