MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS157
Study Title	Untargeted metabolome analysis of foods using LC-MS (1)
Study Description	Untargeted metabolome analyses of foods were performed using LC-MS. Food items were selected from the Standard Tables of Food Composition in Japan-2005 (Seventh Revised Version) published by the Ministry of Education, Culture, Sports, Science and Technology, Japan (hereafter, refered to as the standard table). Metabolites in foods were extracted with methanol, separated by reversed-phase LC and detected using a high-resolution mass spectrometry (LTQ-FT, ThermoFisher Scientific). Two different conditions (Method 1, and Method 5) were applied to ESI positive mode detections, and Method 1 was applied to ESI negative mode detection. A series of different parameter settings for PowerGetBatch software were used for peak detection, and valid peaks were selected by an alignment of the resulted peaks with those detected from several mock samples. The detailed peak information including the results from compound database search and prediction of flavonoid aglycones using FlavonoidSearch were published from the Food Metabolome Repository (http://metabolites.in/foods).

Experimental Design	organism part comparison design
Experimental Factor Name	food
Experimental Factor Type	food

Person Last Name	Sakurai
Person First Name	Nozomu
Person Mid Initials
Person Affiliation	National Institute of Genetics, Kazusa DNA Research Institute
Person Roles	submitter

PubMed ID
Publication DOI

Protocol Name	Sample collection	Extraction	Chromatography	Mass spectrometry Positive Method 1	Mass spectrometry Positive Method 5	Mass spectrometry Negative Method 1	Data processing	Metabolite identification
Protocol Type	Sample collection	Extraction	Chromatography	Mass spectrometry	Mass spectrometry	Mass spectrometry	Data processing	Metabolite identification
Protocol Description	Foods without 'Removed Portion' were ground into fine powder in liquid nitrogen. 'Removed Portion' described in the 'Remarks' in the Standard Tables were removed. Solid samples were ground into fine powder in liquid nitrogen with mortal and pestle. When food size is large, a representative portion is cutout and ground. For example, in the case of a water melon, a portion of comb cut where the edge is along to the line between the petiole and the tip of the fruit is used to minimize the deviation of maturity in the fruit. Liquid samples are used without grinding. Water instead of the sample materials was used for Mock samples.	"Compounds in foods were extracted by approximately 75%(v/v) methanol. In the case of liquid samples and powders from foods containing abundant water (such as vegetables), 3 times volume (v/v or w/v) of 100% methanol were added. In the case of samples with low water content (such as dried seaweed), 400 times volume (w/v) of 75% methanol were added. We did not measure the moisture content of each food. A 25 µM of 7-hydroxy-5-methylflavone is contained as internal standard (IS) in the added methanol. The sample in methanol in 2 mL tubes was homogenized using Mixer Mill MM 300 (QIAGEN) at 25 Hz, for 2 min, twice. A homogenate was centrifuged under 17,400 x g, 5 min at 4 ℃. A supernatants was passed through a Polytetrafluoroethylene (PTFE) filter (pore size 0.2 µm, Millipore), and a filtrate was applied to a C18 silica column (MonoSpin C18, GL Science) to remove highly-hydrophobic contaminants. The filtrate passed through the C18 column was used for LC-MS analyzes.
The same extraction procedure were performed using 75%(v/v) methanol without sample to prepare mock samples and used as negative controls."	Agilent 1100 system (Agilent) and Finnigan LTQ-FT (Thermo Fisher Scientific) were used. Aliquots (20 µL) of the methanol extract were applied to a TSK-gel ODS-100V column (4.6 x 250 mm, 5 µm, TOSO), and separated by water containing 0.1%(v/v) formic acid (Solvent A) and acetonitrile containing 0.1%(v/v) formic acid (Solvent B). 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 at 0.25 mL/min for 0-100 min, and 0.5 mL/min for 100.1-107 min. The column oven temperature was set to 40 ℃. To monitor the HPLC eluate, a photodiode array detector was used with a wavelength range of 200-650 nm.	Electrospray ionization (ESI)-positive mode with a spray voltage of 4.0 kV and capillary temperature of 300 ℃ was used for compound detection. The nitrogen sheath gas and auxiliary gas were set at 40 and 15 arbitrary units, respectively. The MS scan was set as Full scan: Resolution = 100,000 by Fourier-transform ion cyclotron resonance (FT) MS, MS2 scan: Data dependent scan by ion trap (IT) MS for the most intense 5 ions in the full scan. The dynamic exclusion settings for MS2 scan was follows: repeat count, 3; repeat duration, 30s; exclusion list size, 500; margin, 10 ppm, exclusion duration, 20s. A m/z range for Full scan was set to 100-1500. Raw data were obtained by Xcalibur software (ver. 2.0.7, Thermo Fisher Scientific).	Electrospray ionization (ESI)-positive mode with a spray voltage of 4.0 kV and capillary temperature of 300 ℃ was used for compound detection. The nitrogen sheath gas and auxiliary gas were set at 40 and 15 arbitrary units, respectively. The MS scan was set as Full scan: Resolution = 12,500 by FT, MS2 scan: Data dependent scan by IT for the most intense 5 ions in the full scan, and MS3 scan: Data dependent scan by IT for the most intense 2 ions in the MS2 scan. The dynamic exclusion settings for MS2 scan was follows: repeat count, 3; repeat duration, 30s; exclusion list size, 500; margin, 10 ppm, exclusion duration, 20s. A m/z range for Full scan was set to 100-1500. Raw data were obtained by Xcalibur software (ver. 2.0.7, Thermo Fisher Scientific).	Electrospray ionization (ESI)-negative mode with a spray voltage of 4.0 kV and capillary temperature of 300 ℃ was used for compound detection. The nitrogen sheath gas and auxiliary gas were set at 40 and 15 arbitrary units, respectively. The MS scan was set as Full scan: Resolution = 100,000 by Fourier-transform ion cyclotron resonance (FT) MS, MS2 scan: Data dependent scan by ion trap (IT) MS for the most intense 5 ions in the full scan. The dynamic exclusion settings for MS2 scan was follows: repeat count, 3; repeat duration, 30s; exclusion list size, 500; margin, 10 ppm, exclusion duration, 20s. A m/z range for Full scan was set to 100-1500. Raw data were obtained by Xcalibur software (ver. 2.0.7, Thermo Fisher Scientific).	Data not submitted.	Data not submitted.
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	Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer	Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer
Protocol Hardware			Agilent 1100 HPLC (Agilent Technologies) HPLC equipped with photodiode array detector	LTQ-FT (Thermo Fisher Scientific) Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS)	LTQ-FT (Thermo Fisher Scientific) Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS)	LTQ-FT (Thermo Fisher Scientific) Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS)
Protocol Software				Xculibur 2.0.7 (Thermo Fisher Scientific, Waltham, MA, USA)	Xculibur 2.0.7 (Thermo Fisher Scientific, Waltham, MA, USA)	Xculibur 2.0.7 (Thermo Fisher Scientific, Waltham, MA, USA)

Public Release Date	2022-08-25

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

SDRF File	MTBKS157.sdrf.txt

Comment[Study type]	untargeted metabolite profiling
Comment[Experiment type]	liquid chromatography-mass spectrometry
Comment[Submission type]	LC-DAD-MS
Comment[BioProject]	PRJDB13827
Comment[Related study]	Metabolonote:SE112
Comment[Contributor]	Kunihiro Suda, Nayumi Akimoto, Sachiko Osawa (Kazusa DNA Research Institute)
Comment[Submission Date]	2022-07-01
Comment[Last Update Date]	2022-09-02