MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS61
Study Title	Synechocystis sp. metabolite analysis
Study Description	Investigation of cyanobacteria Synechocystis sp. PCC6803 metabolites. 3 replicates data are examined.

Experimental Design	species design
Experimental Factor Name
Experimental Factor Type

Person Last Name	Ara
Person First Name	Takeshi
Person Mid Initials
Person Affiliation	Kazusa DNA Research Institute
Person Roles	submitter

PubMed ID
Publication DOI

Protocol Name	Sample collection	Extraction	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Type	Sample collection	Extraction	Chromatography	Mass spectrometry	Data processing	Metabolite identification
Protocol Description	Synechocystis sp. PCC6803 are grown in the BG11 culture medium in an incubator (150rpm).	Harvested sample is frozen by liquid N2 and resulting powder (100mg) are solved in 500 microL 80% methanol solution. Cells are homogenized by TissueLyser (QUIAGEN) and centrifuged (15000rpm, 10min, 4 degree C). 20 microL of the supernatant (300 microL) is injected into HPLC after 0.2 micrometre membrane filter treatment.	Instrument: Agilent 1200 HPLC (Agilent Technologies) HPLC equipped with photodiode array detector; Comment: Elute monitoring by PDA equipped with Agilent 1200 LC (Agilent Technologies) in 2 nm step.; Max wave length for elute monitering: 600.0 nm; Min wave length for elute monitering: 200.0 nm; Column name: TSKgel Amide-80 (4.6 x 250 mm, 5 micrometer; TOSOH); Column temperature: 40.0 degree C; Elute monitor: photodiode array detector; Flow gradient: 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); Flow rate: 0.8 ml/min; Solvent: A; 0.1% formic acid aq. B; ACN (addition 0.1% formic acid fc.)	Instrument: LTQ-Orbitrap XL (Thermo Fisher Scientific) Hybrid linear ion trap (LTQ)/orbitrap mass spectrometer; MS scan setting: Xcalibur scan setting: 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).; Data processing software: Xcalibur 2.0 (Thermo Fisher Scientific, Waltham, MA, USA); Fragmentation method: Collision Induced Dissociation (CID); Ion isolation: ESI; Ion mode: Positive; Mass analyser: LTQ-Orbitrap; Resolution: 60000; Scan mass range: m/z 150.0-2000.0	Xcalibur 2.0 (Thermo Fisher Scientific, Waltham, MA, USA); PowerGet analysis for annotation of peaks with MS/MS : 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.	In annotation process, KEGG, KNApSAcK and LipidMAPS are used for primary database search. Peaks with no hit to these databases are then selected to secondary search using exactMassDB and Pep1000 databases. After the database search processes, each database hits are manually checked to assign a compound name or compound category name. In case of no compound name or compound category name can assign, predicted molecular formulas are used for the annotation. Peaks without predicted molecular formula are assigned as "unidentified" peak.
Protocol Parameters		Post extraction;Derivatization	Chromatography instrument;Autosampler model;Column model;Column type;Guard column;Detector;Signal range;Resolution	Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer
Protocol Hardware			Agilent 1200 HPLC (Agilent Technologies) HPLC equipped with photodiode array detector	LTQ-Orbitrap XL (Thermo Fisher Scientific) Hybrid linear ion trap (LTQ)/orbitrap mass spectrometer
Protocol Software				Xcalibur 2.0 (Thermo Fisher Scientific, Waltham, MA, USA)	Xcalibur 2.0 (Thermo Fisher Scientific, Waltham, MA, USA); PowerGet(Sakurai et al., BioMed Research International, 2014:194812)	PowerGet(Sakurai et al., BioMed Research International, 2014:194812)

Public Release Date	2024-06-14

Term Source Name	Metabolonote
Term Source File	http://metabolonote.kazusa.or.jp
Term Source Version

SDRF File	MTBKS61.sdrf.txt

Comment[Study type]	untargeted metabolite profiling
Comment[Experiment type]	liquid chromatography-mass spectrometry	orbitrap
Comment[Submission type]	LC-DAD-MS
Comment[BioProject]	PRJDB14159
Comment[Related study]	Metabolonote:SE6
Comment[Contributor]	Hideki Nagasaki, Sachiko Osawa, Hideki Hirakawa, Norimoto Shimada, Mitsuo Enomoto, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata (Kazusa DNA Research Institute)
Comment[Submission Date]	2019-10-05
Comment[Last Update Date]	2024-06-14
