Summary of Study ST001874

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	ST001874
Study Title	Metabolomics analysis of multiple samples on Agilent 6546-Part 1
Study Type	Metabolomics
Study Summary	Metabolomics analysis of multiple samples from human, trying to annotate the metabolites in them. Agilent 6546 LC-QTOF 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)	d
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:	SU001951
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
SA174797	Blood-15V-1	Blood	15V
SA174798	Blood-15V-6	Blood	15V
SA174799	Blood-15V-5	Blood	15V
SA174800	Blood-15V-2	Blood	15V
SA174801	Blood-15V-3	Blood	15V
SA174802	Blood-15V-4	Blood	15V
SA174803	Blood-30V-6	Blood	30V
SA174804	Blood-30V-5	Blood	30V
SA174805	Blood-30V-2	Blood	30V
SA174806	Blood-30V-1	Blood	30V
SA174807	Blood-30V-4	Blood	30V
SA174808	Blood-30V-3	Blood	30V
SA174809	Blood-45V-6	Blood	45V
SA174810	Blood-45V-5	Blood	45V
SA174811	Blood-45V-2	Blood	45V
SA174812	Blood-45V-4	Blood	45V
SA174813	Blood-45V-1	Blood	45V
SA174814	Blood-45V-3	Blood	45V
SA174815	HepG2-15V-5	HepG2 cells	15V
SA174816	HepG2-15V-6	HepG2 cells	15V
SA174817	HepG2-15V-4	HepG2 cells	15V
SA174818	HepG2-15V-3	HepG2 cells	15V
SA174819	HepG2-15V-1	HepG2 cells	15V
SA174820	HepG2-15V-2	HepG2 cells	15V
SA174821	HepG2-30V-5	HepG2 cells	30V
SA174822	HepG2-30V-6	HepG2 cells	30V
SA174823	HepG2-30V-4	HepG2 cells	30V
SA174824	HepG2-30V-1	HepG2 cells	30V
SA174825	HepG2-30V-3	HepG2 cells	30V
SA174826	HepG2-30V-2	HepG2 cells	30V
SA174827	HepG2-45V-6	HepG2 cells	45V
SA174828	HepG2-45V-5	HepG2 cells	45V
SA174829	HepG2-45V-4	HepG2 cells	45V
SA174830	HepG2-45V-1	HepG2 cells	45V
SA174831	HepG2-45V-2	HepG2 cells	45V
SA174832	HepG2-45V-3	HepG2 cells	45V
SA174833	Urine-15V-5	Urine	15V
SA174834	Urine-15V-4	Urine	15V
SA174835	Urine-15V-6	Urine	15V
SA174836	Urine-15V-3	Urine	15V
SA174837	Urine-15V-1	Urine	15V
SA174838	Urine-15V-2	Urine	15V
SA174839	Urine-30V-5	Urine	30V
SA174840	Urine-30V-4	Urine	30V
SA174841	Urine-30V-6	Urine	30V
SA174842	Urine-30V-3	Urine	30V
SA174843	Urine-30V-1	Urine	30V
SA174844	Urine-30V-2	Urine	30V
SA174845	Urine-45V-6	Urine	45V
SA174846	Urine-45V-5	Urine	45V
SA174847	Urine-45V-3	Urine	45V
SA174848	Urine-45V-1	Urine	45V
SA174849	Urine-45V-2	Urine	45V
SA174850	Urine-45V-4	Urine	45V

Showing results 1 to 54 of 54

Showing results 1 to 54 of 54

Collection:

Collection ID:	CO001944
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.
Sample Type:	Blood (plasma), Urine, HepG2 cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001963
Treatment Summary:	No treatment

Sample Preparation:

Sampleprep ID:	SP001957
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:

SP001957

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	AN003036
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent 1290 Infinity
Column	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Agilent 6456 Q-TOF
Ion Mode	POSITIVE
Units	peak area

Chromatography:

Chromatography ID:	CH002249
Instrument Name:	Agilent 1290 Infinity
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:	MS002823
Analysis ID:	AN003036
Instrument Name:	Agilent 6456 Q-TOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	the capillary voltage was 3.5 kV, the sheath gas temperature and gas temperature were 350 and 325 °C, respectively. Sheath gas flow and gas flow were 11 and 7 L/min, respectively. Nebulizer was set as 35 psi. The data was processed by XCMS, MS-DIAL, MZmine 2 and MetEx.
Ion Mode:	POSITIVE