SE5:/S01/M02/D01

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Sample Set Information

ID SE5
Title Physcomitrella patens metabolite analysis
Description Investigation of Physcomitrella patens subsp. patens metabolites. 4 replicates data are examined for each sample.
Authors Norimoto Shimada, Takeshi Ara, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daiskue Shibata, Kazusa DNA Research Institute
Reference Direct Submittion
Comment version 4


SE5 S01 200.jpg

Photo: Physcomitrella patens subsp. patens (same clone of harvested sample (S01))(Aug 2013).

Sample Information

ID S01
Title Physcomitrella patens subsp. patens
Organism - Scientific Name Physcomitrella patens subsp. patens
Organism - ID NCBI taxonomy:145481
Compound - ID
Compound - Source
Preparation Physcomitrella patens subsp. patens are grown on plant culture box filled by 1/2MS culture with 0.5% phytogel in an incubator with 18h Light/6h Dark and 24.6 degree C condition. Whole plants are harvested.
Sample Preparation Details ID
Comment [KomicMarket ID] KSBA_26

Analytical Method Information

ID M02
Title LC-FTICR-MS, ESI Positive analysis
Method Details ID MS1
Sample Amount 6.7mg
Comment [MassBase ID] MDLC1_25861


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

ID MS1
Title LC-FT-ICR-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 Harvested sample is frozen by liquid N2 and resulting powder (100mg) are solved in 300uL methanol solution. 20uL sample is injected into HPLC after 0.2um membrane filter treatment. HPLC conditions: Agilent 1100 series (Agilent), Column: TSKgel-100V (4.6 x 250 mm, 5 micrometer; TOSOH), Solvent: A; 0.1% formic acid aq. B; ACN (addition 0.1% formic acid fc.), Gradient: (B);3% (0.0 to 1.0 min), 3 to 30% (1.0 to 26.0 min), 50 to 90% (26.0 to 41.0 min), 90% to 100% (41.1 to 46.0 min), 100% (46.1 to 51.0 min), 3% (51.1 to 58.0 min), Column temp.: 40 degree C, Flow rate=0.5mL/min, PDA: 200-650 nm (2 nm step). FT-ICR-MS conditions: Filter 1: FTMS + c norm !corona !pi res=100000 o(150.0-2000.0); 2: ITMS + c norm !corona !pi Dep MS/MS Most intense ion from (1); 3: ITMS + c norm !corona !pi Dep MS/MS 2nd most intense ion from (1); 4: ITMS + c norm !corona !pi Dep MS/MS 3rd most intense ion from (1).
Comment_of_details

Data Analysis Information

ID D01
Title PowerGet data analysis for Bio-MassBank
Data Analysis Details ID DS1
Recommended decimal places of m/z 6|ITMS 2
Comment


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The mass spectrum data are available at Bio-MassBank.

Data Analysis Details Information

ID DS1
Title PowerGet analysis for annotation of peaks with MS/MS (A3)
Description Raw data files are converted to text file by MSGet software without cut off value and peaks are extracted from the text files by PowerFT with parameters (intensity cut off=5000, peak selection filter is default, intensity cut off in peak assignment=1000). The replicates data are aligned by PowerMatch with blank data. The alignment is manually edited. Assigned peaks observed in multiple replicate samples are selected for annotation process. Assigned peaks with clear MS2 data are selected for the registration of Bio-MassBank.
Comment_of_details
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