# id kazusa:SE1_S01_M01_D01.info.txt sample_set id SE1 title Arabidopsis thaliana leaf metabolite analysis description Investigation of Arabidopsis thaliana leaf metabolites. 6 replicates (for extraction) data are examined for each sample. authors Takeshi Ara, Ryosuke Sasaki, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Kazusa DNA Research Institute reference Direct Submittion comment version 7 sample id S01 title Arabidopsis wt leaf organism_scientific_name Arabidopsis thaliana organism_id NCBI taxonomy:3702 preparation Arabidopsis thaliana Col-0 seeds are sown on pots filled by vemiculite and are grown in an incubator with 18h Light/6h Dark and 22 degree C condition. After 2 months later, all leaves are harvested. analytical_method id M01 title LC-FTICR-MS, ESI Positive analysis analytical_method_details_id MS1 sample_amount 6.7 mg data_analysis id D01 title PowerGet data analysis for Bio-MassBank data_analysis_details_id DS1 recommended_decimal_places_of_mass 6 analytical_method_details 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_method ESI ion_mode Positive description Harvested sample is frozen by liquid N2 and resulting powder (100mg) are solved in 300uL 80% 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 to 30% (0.0 to 25.0 min), 30 to 90% (25.0 to 40.0 min), 90% (40.0 to 45.0 min), 95% (45.1 to 50.0 min), 3% (50.1 to 57.0 min), Column temp.: 30 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(200.0-1500.0); 2: ITMS + c norm !corona !pi Dep MS/MS Most intense ion from (1)., Rejected mass=256.2000;266.0000;284.2000;300.2000;328.2000;344.2000;372.2000;388.2000;416.3000;432.3000;460.0000. comment_of_details [column] TSKgel-100V (4.6 x 250 mm, 5 micrometer; TOSOH) [gradient] Solvent: A; 0.1% formic acid aq. B; ACN (addition 0.1% formic acid fc.), Gradient: (B);3 to 30% (0.0 to 25.0 min), 30 to 90% (25.0 to 40.0 min), 90% (40.0 to 45.0 min), 95% (45.1 to 50.0 min), 3% (50.1 to 57.0 min) [total separation time] 60 min data_analysis_details id DS1 title PowerGet analysis for annotation of peaks with MS/MS (A2) 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, peak shape is manually checked for peaks with intensity < 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 manually selected for the registration of Bio-MassBank.