From Metabolonote
jump-to-nav Jump to: navigation, search

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

Link icon article.png

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

Sample Preparation Details Information

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.

Analytical Method Information

ID M011
Title Method 1: ESI Positive, Data dependent MS2 scan (FT, IT)
Method Details ID MS1
Sample Amount 5 mg / 20 ul injection
Comment Extractions were triplicated from the same sample and equal volume of the extracts were added and analyzed.

[MassBase ID] MDLC1_48041

Link icon database.png Link icon massbase.png

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 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

Data Analysis Information

Title Data analysis using PowerGetBatch
Data Analysis Details ID DS3
Recommended decimal places of m/z default
Comment The data from S02_M01, S02_M02, S02_M03 were used as mock sample data.

Data Analysis Details Information

Title PowerGetBatch 3: manual curation
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 results were exported to text files in TogoMD format.

Personal tools
View and Edit Metadata