Summary of Study ST001873

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001182. The data can be accessed directly via it's Project DOI: 10.21228/M8XD6P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST001873
Study Title	Metabolomics analysis of multiple samples on AB 5600-Part 1
Study Type	Metabolomics
Study Summary	Metabolomics analysis of multiple samples from human, trying to annotate the metabolites in them. AB SCIEX 5600+ was used for metabolomics detection.
Institute	Dalian Institute Of Chemical Physics
Laboratory	Laboratory of High Resolution Separation/Analysis and Metabonomics
Last Name	Zheng
First Name	Fujian
Address	No. 457 Zhongshan Road, Shahekou District, Dalian, Liaoning Province, China
Email	zhengfj@dicp.ac.cn
Phone	18698730176
Submit Date	2021-06-18
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2021-07-24
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001182
Project DOI:	doi: 10.21228/M8XD6P
Project Title:	Metabolomics analysis of multiple samples
Project Summary:	Liquid chromatography–high resolution mass spectrometry (LC-HRMS) is the most popular platform for untargeted metabolomics methods, but annotating LC-HRMS data is a long-standing bottleneck that we are facing since years ago in metabolomics research. A wide variety of methods have been established to deal with the annotation issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for metabolomics and exposome community. Herein, we developed a user-friendly and powerful stand-alone software, MetEx, to enable implementation of classical peak detection-based annotation and a brand-new annotation method based on targeted extraction algorithms. Especially the newly proposed annotation method of targeted extraction can identify more than 2 times more metabolites than traditional peak detection-based annotation methods because it reduces the loss of metabolite signal in the data preprocessing process.
Institute:	Dalian Institute of Chemical Physics
Laboratory:	Laboratory of High Resolution Separation/Analysis and Metabonomics
Last Name:	Zheng
First Name:	Fujian
Address:	457 Zhongshan Road Dalian, China 116023, Dalian, Liaoning, 116021, China
Email:	zhengfj@dicp.ac.cn
Phone:	18698730176

Subject:

Subject ID:	SU001950
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Source	MS2 CE
SA174785	Blank-15V	Blank	15V
SA174786	Blank-30V	Blank	30V
SA174787	Blank-45V	Blank	45V
SA174788	NIST SRM 1950-15V	Blood	15V
SA174789	NIST SRM 1950-30V	Blood	30V
SA174790	NIST SRM 1950-45V	Blood	45V
SA174791	HepG2 cells-15V	Hep G2 cells	15V
SA174792	HepG2 cells-30V	Hep G2 cells	30V
SA174793	HepG2 cells-45V	Hep G2 cells	45V
SA174794	Human urine-15V	Urine	15V
SA174795	Human urine-30V	Urine	30V
SA174796	Human urine-45V	Urine	45V

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001943
Collection Summary:	NIST SRM 1950 was purchased from NIST, and HepG2 cells were purchased from the Chinese Tissue Culture Collections (CTCC, Shanghai, China). Urine was collected from volunteers. Six- to eight-week-old male C57BL/6 mice were fed a regular standard breeding diet and housed under standard pathogen-free (SPF) conditions. Faecal samples and liver tissue were collected and immediately stored at -80 °C for further analysis.
Sample Type:	Blood (plasma), Urine, HepG2 cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001962
Treatment Summary:	No treatment

Sample Preparation:

Sampleprep ID:	SP001956
Sampleprep Summary:	Plasma (NIST SRM 1950): A 240 μL volume of Mix-IS-ACN was added to 60 μL of NIST SRM 1950 for protein precipitation. Then, the sample was vortexed for 60 s and centrifuged for 10 min at 15,000 g and 4 °C. Then, 250 μL of supernatant was transferred to a new centrifuge tube for lyophilization. The residue was reconstituted with 60 μL of 90% H2O/CH3OH (v/v). Urine: A 60 μL sample of urine was centrifuged for 10 min at 15,000 g and 4 °C, and the supernatant was transferred to a new centrifuge tube. Then, 30 μL Mix-IS-MeOH was added to the same centrifuge tube, and the mixture was thoroughly combined on a vortex mixer for 60 s. HepG2: HepG2 cells were purchased from the Chinese Tissue Culture Collections (CTCC, Shanghai, China) and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 IU/ml penicillin and 100 µg/ml streptomycin (Gibco). These cells were cultured at 37 °C in a humidified 5% CO2 atmosphere and treated within 24 hours after the confluence of cells reached 80%. The culture media of the cells was removed, and the cells were washed three times in phosphate-buffered saline (PBS). Then, the cells were quickly frozen in liquid nitrogen and stored at -80 °C before extraction. Then, 1 mL 80% CH3OH/H2O (v/v) was added to the cells, and the cells were scraped with extraction solvent. Both the extract and cell/debris suspension were transferred to a clean tube and thoroughly mixed on a vortex mixer for 120 s. Ultrasonication at 30 Hz for 2 × 10 s was performed. After being allowed to settle for 10 min, the cell extraction solution was centrifuged for 15 min at 15,000 g and 4 °C. Then, 800 μL of supernatant was transferred to a new centrifuge tube for lyophilization. The residue was reconstituted with 40 μL of Mix-IS-MeOH.

Sampleprep ID:

SP001956

Sampleprep Summary:

Plasma (NIST SRM 1950): A 240 μL volume of Mix-IS-ACN was added to 60 μL of NIST SRM 1950 for protein precipitation. Then, the sample was vortexed for 60 s and centrifuged for 10 min at 15,000 g and 4 °C. Then, 250 μL of supernatant was transferred to a new centrifuge tube for lyophilization. The residue was reconstituted with 60 μL of 90% H2O/CH3OH (v/v). Urine: A 60 μL sample of urine was centrifuged for 10 min at 15,000 g and 4 °C, and the supernatant was transferred to a new centrifuge tube. Then, 30 μL Mix-IS-MeOH was added to the same centrifuge tube, and the mixture was thoroughly combined on a vortex mixer for 60 s. HepG2: HepG2 cells were purchased from the Chinese Tissue Culture Collections (CTCC, Shanghai, China) and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 IU/ml penicillin and 100 µg/ml streptomycin (Gibco). These cells were cultured at 37 °C in a humidified 5% CO2 atmosphere and treated within 24 hours after the confluence of cells reached 80%. The culture media of the cells was removed, and the cells were washed three times in phosphate-buffered saline (PBS). Then, the cells were quickly frozen in liquid nitrogen and stored at -80 °C before extraction. Then, 1 mL 80% CH3OH/H2O (v/v) was added to the cells, and the cells were scraped with extraction solvent. Both the extract and cell/debris suspension were transferred to a clean tube and thoroughly mixed on a vortex mixer for 120 s. Ultrasonication at 30 Hz for 2 × 10 s was performed. After being allowed to settle for 10 min, the cell extraction solution was centrifuged for 15 min at 15,000 g and 4 °C. Then, 800 μL of supernatant was transferred to a new centrifuge tube for lyophilization. The residue was reconstituted with 40 μL of Mix-IS-MeOH.

Combined analysis:

Analysis ID	AN003035
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Waters Acquity
Column	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Triple TOF
MS instrument name	ABI Sciex 5600+ TripleTOF
Ion Mode	POSITIVE
Units	peak area

Chromatography:

Chromatography ID:	CH002248
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Column Temperature:	50
Flow Rate:	0.35 mL/min
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002822
Analysis ID:	AN003035
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
MS Comments:	The spray voltage was 5.5 kV and the source temperature was 550 °C, Curtain gas, gas 1 and gas 2 were set at 35, 55, and 55 psi, respectively. The data was processed by XCMS, MS-DIAL, MZmine 2 and MetEx.
Ion Mode:	POSITIVE