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.

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Study IDST001873
Study TitleMetabolomics analysis of multiple samples on AB 5600-Part 1
Study TypeMetabolomics
Study SummaryMetabolomics 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
LaboratoryLaboratory of High Resolution Separation/Analysis and Metabonomics
Last NameZheng
First NameFujian
AddressNo. 457 Zhongshan Road, Shahekou District, Dalian, Liaoning Province, China
Emailzhengfj@dicp.ac.cn
Phone18698730176
Submit Date2021-06-18
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-07-24
Release Version1
Fujian Zheng Fujian Zheng
https://dx.doi.org/10.21228/M8XD6P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA174785Blank-15VBlank 15V
SA174786Blank-30VBlank 30V
SA174787Blank-45VBlank 45V
SA174788NIST SRM 1950-15VBlood 15V
SA174789NIST SRM 1950-30VBlood 30V
SA174790NIST SRM 1950-45VBlood 45V
SA174791HepG2 cells-15VHep G2 cells 15V
SA174792HepG2 cells-30VHep G2 cells 30V
SA174793HepG2 cells-45VHep G2 cells 45V
SA174794Human urine-15VUrine 15V
SA174795Human urine-30VUrine 30V
SA174796Human urine-45VUrine 45V
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.

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 QTOF
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:QTOF
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
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