MAGE-TAB Version	1.1
Comment[MetaboBank accession]	MTBKS214
Study Title	LC-MS-based metabolome analysis of persons with type 2 diabetes with or without diabetic complications
Study Description	"We profiled serum metabolites of persons with T2D with or without diabetic complications using a comprehensive non-targeted metabolomics approach with liquid chromatograph-mass spectrometry.
*** Related data are to be made available through the controlled-access database JGA (study accession JGAS000572). ***"

Experimental Design	case control design
Experimental Factor Name	complications
Experimental Factor Type	complications

Person Last Name	Suzuki	Yamauchi	Okada
Person First Name	Ken	Toshimasa	Yukinori
Person Mid Initials
Person Affiliation	Osaka University	The University of Tokyo	Osaka University
Person Roles	submitter	submitter	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	Serum samples from the participants were collected at collaborating facilities.	"Metabolite extraction and metabolome analysis were conducted at Human Metabolome Technologies (HMT), Japan.
For LC-TOFMS analysis, 500 μl of serum was added to 1500 μl of 1% formic acid/acetonitrile containing internal standard solution (Solution ID: H3304-1002, HMT) at 0°C to inactivate enzymes. D-camphor-10-sulfonic acid was used for the internal standard in both the positive and negative modes. The solution was thoroughly mixed and centrifuged at 2300 × g and 4°C for 5 min. The supernatant was filtrated by using Hybrid SPE phospholipid (55261-U, Supelco, Bellefonte, PA, USA) to remove phospholipids. The filtrate was desiccated and dissolved with 100 μl of iso-propanol/Milli-Q for LC-MS analysis."	LC analysis was carried out using an Agilent LC System (Agilent 1200 series RRLC system SL) equipped with an Agilent 6230 TOF MS (Agilent Technologies) in HMT. The systems were controlled by Agilent G2201AA ChemStation software version B.03.01 (Agilent Technologies) equipped with an ODS column (2 × 50 mm, 2 μm). The equilibration time was 7.5 minutes.	TOF MS analysis was carried out using an Agilent LC System (Agilent 1200 series RRLC system SL) equipped with an Agilent 6230 TOF MS (Agilent Technologies) in HMT. The spectrometer was scanned from m/z 50 to 1000.	"Peaks were extracted using MasterHands, automatic integration software (Keio University, Tsuruoka, Yamagata, Japan) to obtain peak information including m/z, peak area, and retention time for LC-TOFMS measurement (RT). Signal peaks corresponding to isotopomers, adduct ions, and other product ions of known metabolites were excluded. The remaining peaks were annotated according to the HMT metabolite database based on their m/z values with the MTs and RTs determined by TOFMS. Areas of the annotated peaks were normalized based on the levels of the internal standard for each modality (LC-TOFMS, D-camphor-10-sulfonic acid) and sample amounts to obtain relative levels of each metabolite.
Metabolite identification data are to be made available through the controlled-access database JGA (study accession JGAS000572).
The normalized metabolite abundances were regressed to the presence of the complications with the logistics regression model as implemented in the glm() function in the R. (BETA = Effect sizes in the logistic regression analysis; SE = standard errors in the logistic regression analysis; P = P-values (Wald's test) in the logistic regression analysis; q = P-values corrected by Benjamini-Hochberg method)"	Metabolite identification data are to be made available through the controlled-access database JGA (study accession JGAS000572).
Protocol Parameters		Post extraction;Derivatization	Chromatography instrument;Autosampler model;Column model;Column type;Guard column	Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer
Protocol Hardware
Protocol Software

Public Release Date	2022-11-02

Term Source Name
Term Source File
Term Source Version

SDRF File	MTBKS214.sdrf.txt

Comment[Study type]	untargeted metabolite profiling
Comment[Experiment type]	liquid chromatography-mass spectrometry
Comment[Submission type]	LC-MS
Comment[BioProject]	PRJDB14622
Comment[Related study]	JGA:JGAS000572	NBDC:hum0372
Comment[NBDC]	The Data Access Committee of the National Bioscience Database Center (NBDC) approved that this personal data was made published according to the NBDC Guidelines for Human Data Sharing (https://humandbs.biosciencedbc.jp/en/guidelines/data-sharing-guidelines ) as the NBDC Research ID hum0372 and the application ID J-DS000220-015.
Comment[Contributor]
Comment[Submission Date]	2022-10-13
Comment[Last Update Date]	2022-11-04