SE7:/S01/M03/D01

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Sample Set Information

ID SE7
Title Chlamydomonas reinhardtii metabolite analysis
Description Investigation of Chlamydomonas reinhardtii C-9 metabolites. 3 replicates data are examined.
Authors Takeshi Ara, Norimoto Shimada, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute
Reference Direct Submittion
Comment version 1


Link icon database.png Link icon pgdbj.png

The web resources and information related to the species used in this study are available at Plant Genome Database Japan (PGDBj).

http://pgdbj.jp/plantdb/plantinfo.html?ln=en&cmd=entry&ppid=t3055

Sample Information

ID S01
Title Chlamydomonas reinhardtii C-9
Organism - Scientific Name Chlamydomonas reinhardtii
Organism - ID NCBI taxonomy:3055
Compound - ID
Compound - Source
Preparation Chlamydomonas reinhardtii C-9 mt- are grown in the TAP culture medium in an incubator with Light at all times condition (28 degree C, 150rpm). The strain is provided from Dr Hideya Fukuzawa, Kyoto Univ.
Sample Preparation Details ID
Comment [KomicMarket ID] KSBA_28

Analytical Method Information

ID M03
Title LC-Orbitrap-MS, ESI Positive analysis
Method Details ID MS1
Sample Amount 6.7mg
Comment [MassBase ID] MDLC1_18902


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

Analytical Method Details Information

ID MS1
Title LC-Orbitrap-MS ESI positive method 1
Instrument Agilent1100 HPLC (Agilent), LTQ-Orbitrap (Thermo Fisher Scientific)
Instrument Type LC-Orbitrap-MS
Ionization ESI
Ion Mode Positive
Description Harvested sample is frozen by liquid N2 and resulting powder (100mg) are solved in 500uL 80% methanol solution. Cells are homogenized by TissueLyser (QUIAGEN) and centrifuged (15000rpm, 10min, 4 degree C). 20uL of the supernatant (300uL) is injected into HPLC after 0.2um membrane filter treatment. HPLC conditions: Agilent 1100 series (Agilent), Column: TSKgel Amide-80 (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);80 to 45% (0.0 to 30.0 min), 45 to 35% (30.0 to 30.1 min), 35% (30.1 to 35.0 min), 35% to 80% (35.0 to 35.1 min), 80% (35.1 to 42.0 min), Column temp.: 40 degree C, Flow rate=0.8mL/min, PDA: 200-600 nm (2 nm step). Orbitrap-MS conditions: Filter 1: FTMS + c norm !corona !pi res=60000 o(150.0-2000.0); 2: FTMS + c norm !corona !pi res=7500 Dep MS/MS Most intense ion from (1); 3: FTMS + c norm !corona !pi res=7500 Dep MS/MS 2nd 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
Comment


Link icon database2.png Link icon biomassbank.png

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 (A4)
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 in peak detection=20000, margin of ion grouping in peak detection=5, 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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