Summary of Study ST001231

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 PR000824. The data can be accessed directly via it's Project DOI: 10.21228/M85Q5K 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 IDST001231
Study TitlePlasma untargeted metabolomics study of pulmonary tuberculosis
Study SummaryIn this study, differentially abundant plasma metabolites were screened by using the ultra-high performance liquid chromatography coupled with Q Exactive mass spectrometry in pulmonary tuberculosis(TB) patients and normal controls(NC) or patients with other pulmonary diseases such as, community-acquired pneumonia(CAP) and lung cancer(LC).
Institute
Zhengjiang University
DepartmentSchool of Medicine
LaboratoryInstitute of Cell Biology
Last NameLi
First NameJi-Cheng
Address866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang Province, 310058, PR China
Emaillijichen@zju.edu.cn
Phone+86-571-88208088
Submit Date2019-08-05
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-12-01
Release Version1
Ji-Cheng Li Ji-Cheng Li
https://dx.doi.org/10.21228/M85Q5K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000824
Project DOI:doi: 10.21228/M85Q5K
Project Title:Pulmonary tuberculosis plasma untargeted metabolomics
Project Type:Untargeted MS analysis
Project Summary:An untargeted metabolomics study on plasma samples from human pulmonary tuberculosis
Institute:Zhengjiang University
Department:School of Medicine
Laboratory:Institute of Cell Biology
Last Name:Li
First Name:Ji-Cheng
Address:866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang Province, 310058, PR China
Email:lijichen@zju.edu.cn
Phone:+86-571-88208088

Subject:

Subject ID:SU001299
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Disease
SA087726FY26CAP
SA087727FY25CAP
SA087728FY24CAP
SA087729FY29CAP
SA087730FY30CAP
SA087731FY33CAP
SA087732FY32CAP
SA087733FY23CAP
SA087734FY19CAP
SA087735FY14CAP
SA087736FY12CAP
SA087737FY11CAP
SA087738FY15CAP
SA087739FY17CAP
SA087740FY34CAP
SA087741FY18CAP
SA087742FY20CAP
SA087743FY36CAP
SA087744FY75CAP
SA087745FY74CAP
SA087746FY72CAP
SA087747FY8CAP
SA087748FY91CAP
SA087749FY98CAP
SA087750FY93CAP
SA087751FY67CAP
SA087752FY60CAP
SA087753FY41CAP
SA087754FY39CAP
SA087755FY42CAP
SA087756FY5CAP
SA087757FY6CAP
SA087758FY52CAP
SA087759FY10CAP
SA087760FY21CAP
SA087761LC64LC
SA087762LC42LC
SA087763LC44LC
SA087764LC41LC
SA087765LC36LC
SA087766LC28LC
SA087767LC34LC
SA087768LC46LC
SA087769LC48LC
SA087770LC63LC
SA087771LC72LC
SA087772LC61LC
SA087773LC56LC
SA087774LC53LC
SA087775LC55LC
SA087776LC23LC
SA087777LC16LC
SA087778LC92LC
SA087779LC95LC
SA087780LC91LC
SA087781LC84LC
SA087782LC74LC
SA087783LC75LC
SA087784LC69LC
SA087785LC67LC
SA087786LC05LC
SA087787LC08LC
SA087788LC14LC
SA087789LC02LC
SA087790LC01LC
SA087791LC09LC
SA087792N_02NC
SA087793N_01NC
SA087794N_36NC
SA087795N_14NC
SA087796N_13NC
SA087797N_11NC
SA087798N_15NC
SA087799N_16NC
SA087800N_18NC
SA087801N_17NC
SA087802N_10NC
SA087803N_09NC
SA087804N_04NC
SA087805N_03NC
SA087806N_05NC
SA087807N_06NC
SA087808N_08NC
SA087809N_07NC
SA087810N_19NC
SA087811N_20NC
SA087812N_31NC
SA087813N_30NC
SA087814N_32NC
SA087815N_33NC
SA087816N_35NC
SA087817N_34NC
SA087818N_29NC
SA087819N_28NC
SA087820N_23NC
SA087821N_22NC
SA087822N_24NC
SA087823N_25NC
SA087824N_27NC
SA087825N_26NC
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Collection:

Collection ID:CO001293
Collection Summary:Morning fasting heparin anti-coagulated blood samples were drawn and centrifuged at 4°C, 3000 r / min for 10 min. The supernatant was aspirated, and frozen at -80°C.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001314
Treatment Summary:No special treatment

Sample Preparation:

Sampleprep ID:SP001307
Sampleprep Summary:The frozen heparin anti-coagulated plasma samples were thawed on ice and 100 μl of each sample was transferred to a 1.5ml sterile micro-centrifugen tube. After the addition of 300 μl of methanol (containing internal standard L-2-chlorophenylalanine 1 μg/ml), each sample was vortexed for 30 s, sonicated for 10 min in ice-water bath, and incubated for 1 h at -20°C to precipitate proteins. Then each sample was centrifuged at 12000 rpm for 15 min at 4°C. The resulting supernatants were transferred to LC-MS vials and stored at -80°C until the UPLC-QE-MS analysis. Each quality control sample was also prepared by mixing an equal aliquot of the supernatants from each sample. The treatment methods were the same as above.

Combined analysis:

Analysis ID AN002048 AN002049
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH001488
Chromatography Summary:The mobile phase A was 0.1% formic acid in water for positive, and 5 mmol/L ammonium acetate in water for negative, and the mobile phase B was acetonitrile. The elution gradient was set as follows: 0 min, 1% B; 1 min, 1% B; 8 min, 99% B; 10 min, 99% B; 10.1 min, 1% B; 12 min, 1% B.
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:0 min, 1% B; 1 min, 1% B; 8 min, 99% B; 10 min, 99% B; 10.1 min, 1% B; 12 min, 1% B.
Solvent A:Pos mode:100% water; 0.1% formic acid, Neg mode:100% water; 5 mM ammonium acetate
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS001900
Analysis ID:AN002048
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:mass range(m/z):70-1000 Convert the mass spectrometry raw data to the mzML format. Then do retention time correction, peak identification, peak extraction, peak integration, peak alignment, etc., and finally compare the database for material identification. ProteoWizard,XCMS,OSI-SMMS,in-house MS/MS database
Ion Mode:NEGATIVE
  
MS ID:MS001901
Analysis ID:AN002049
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:mass range(m/z):70-1000 Convert the mass spectrometry raw data to the mzML format. Then do retention time correction, peak identification, peak extraction, peak integration, peak alignment, etc., and finally compare the database for material identification. ProteoWizard,XCMS,OSI-SMMS,in-house MS/MS database
Ion Mode:POSITIVE
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