Summary of Study ST001873

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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.
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
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 application/zip

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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


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


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 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 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 instrument type QTOF
MS instrument name ABI Sciex 5600+ TripleTOF
Units peak area


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 ID:MS002822
Analysis ID:AN003035
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
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.