Summary of Study ST002044

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 PR001291. The data can be accessed directly via it's Project DOI: 10.21228/M8V12R 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 IDST002044
Study TitleAn observational study of cardiovascular patients in India
Study SummarySerum samples for CVD patients were analyzed by untargeted metabolomics assays to identify prognostic biomarkers.
Institute
Translational Health Science And Technology Institute (THSTI)
Last NameKumar
First NameYashwant
AddressNCR Biotech Science Cluster 3rd Milestone, Faridabad - Gurgaon Rd, Expressway, Faridabad, Haryana 121001, India
Emailyashubt@gmail.com
Phone0129-2876300
Submit Date2021-12-22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-02-08
Release Version1
Yashwant Kumar Yashwant Kumar
https://dx.doi.org/10.21228/M8V12R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001291
Project DOI:doi: 10.21228/M8V12R
Project Title:An observational study of cardiovascular patients in India
Project Summary:Serum samples for CVD patients were analyzed by untargeted metabolomics assays to identify prognostic biomarkers.
Institute:Translational Health Science And Technology Institute (THSTI)
Last Name:Kumar
First Name:Yashwant
Address:NCR Biotech Science Cluster 3rd Milestone, Faridabad - Gurgaon Rd, Expressway, Faridabad, Haryana 121001, India
Email:yashubt@gmail.com
Phone:0129-2876300
Contributors:Sadjad Baygi, Sanjay K Banerjee, Praloy Chakraborty, Dinesh Barupal

Subject:

Subject ID:SU002126
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Gender
SA192043D-45F
SA192044D-50F
SA192045D-53F
SA192046D-43F
SA192047D-52F
SA192048D-38F
SA192049D-30F
SA192050D-188F
SA192051D-37F
SA192052D-100F
SA192053D-185F
SA192054D-176F
SA192055D-78F
SA192056D-95F
SA192057D-156F
SA192058D-168F
SA192059D-61F
SA192060D-59F
SA192061D-152F
SA192062D-57F
SA192063D-153F
SA192064D-27F
SA192065D-108F
SA192066D-15F
SA192067D-17F
SA192068D-19F
SA192069D-20F
SA192070D-14F
SA192071D-13F
SA192072D-130F
SA192073D-9F
SA192074D-10F
SA192075D-122F
SA192076D-120F
SA192077D-18F
SA192078D-24F
SA192079D-155M
SA192080D-132M
SA192081D-154M
SA192082D-140M
SA192083D-137M
SA192084D-131M
SA192085D-133M
SA192086D-139M
SA192087D-160M
SA192088D-161M
SA192089D-159M
SA192090D-158M
SA192091D-157M
SA192092D-129M
SA192093D-141M
SA192094D-142M
SA192095D-148M
SA192096D-162M
SA192097D-136M
SA192098D-147M
SA192099D-145M
SA192100D-146M
SA192101D-149M
SA192102D-150M
SA192103D-134M
SA192104D-143M
SA192105D-144M
SA192106D-151M
SA192107D-138M
SA192108D-135M
SA192109D-174M
SA192110D-193M
SA192111D-194M
SA192112D-195M
SA192113D-192M
SA192114D-191M
SA192115D-187M
SA192116D-189M
SA192117D-190M
SA192118D-196M
SA192119D-197M
SA192120NHF-87M
SA192121NHF-88M
SA192122NHF-89M
SA192123NHF-81M
SA192124NHF-48M
SA192125D-198M
SA192126NHF-15M
SA192127NHF-44M
SA192128D-186M
SA192129D-184M
SA192130D-170M
SA192131D-171M
SA192132D-172M
SA192133D-169M
SA192134D-167M
SA192135D-3M
SA192136D-165M
SA192137D-166M
SA192138D-173M
SA192139D-128M
SA192140D-181M
SA192141D-182M
SA192142D-183M
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Collection:

Collection ID:CO002119
Collection Summary:Serum samples were collected from CVD patients at the Safdarjung Hospital, New Delhi. In all assessments, all individuals were asked to provide complete information regarding personal health history, self-rated health, and family history of diabetes, tobacco use, and physical activity. Ethical approval was obtained at Safdarjung Hospital, New Delhi for sample collection.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002138
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002132
Sampleprep Summary:Serum samples (100µl) should be properly thawed and spin at 5K rpm for one minute, added with 100 % MeOH (300µl, in1:3 ratio) and vortex well (30s), incubated on ice for 10 minutes and then centrifuged at 10K rpm for 10 minutes at 4℃. Equally, transfer the supernatant into two different well-labeled tubes and then speed vacuum dry and stored at -80℃. One set of the tubes is used for the analysis of polar metabolites and the other one is used for the non-polar metabolites. For the reconstitution of polar metabolites, 50% ACN (50 µl) is added into the vacuum dried sample and for nonpolar 15% of MeOH (50 µl) is used. After the addition of reconstitutes, vortex well for 10 min and centrifuged at 10K rpm for 10 minutes at 4℃ and transfer the supernatant (approx. 40-45 µl) into MS vials. Remove 10µl form every sample containing MS vials and pooled together into a 15 ml tube to use as QC. Then, the samples were stored at -80℃ for further analysis.

Combined analysis:

Analysis ID AN003325 AN003326 AN003327 AN003328
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um) Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um) 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 ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Fusion Orbitrap Thermo Fusion Orbitrap Thermo Fusion Orbitrap Thermo Fusion Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units peak height peak height peak height peak height

Chromatography:

Chromatography ID:CH002464
Chromatography Summary:For hydrophilic interaction (HILIC) chromatography, 5 µl of the prepared samples were injected for analysis. An ultimate 3000 UPLC XBridge BHE Amide column (2.1 x 100 mm, 2.5 µm; Waters Corporation) was used and maintained at 35℃ for separation. The mobile phase was delivered at 0.35mL/min. The mobile phase A consisted of 20mM ammonium acetate in the water of pH 9.0 and mobile phase B was 100% acetonitrile. The elution gradient is used as follows: 0 min-85% B, 2 min-10% B, 14 min- 10% B, 14.1 min- 85% B, 16 min- 85%B.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Xbridge BEH HILIC (75 x 2.1mm,2.5um)
Column Temperature:35
Flow Gradient:0 min-85% B, 2 min-10% B, 14 min- 10% B, 14.1 min- 85% B, 16 min- 85%B.
Flow Rate:0.35mL/min
Solvent A:100% water; 20 mM ammonium acetate, pH 9.0
Solvent B:100% acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH002465
Chromatography Summary:For reversed-phase (RP) chromatographic analyses, 5 µL of prepared samples were injected. The separation was performed using a UPLC ultimate 3000 using the HSS T3 column (2.1x 100mm, 1.7 µm; Waters Corporation) at 40℃. The mobile phase was delivered at 300µL/min and consisted of eluent A (water with 0.1%formic acid) and eluent B (acetonitrile with 0.1% formic acid), delivered in a gradient profile: 0min-1% B, 1min-15%B, 4min-35% B, 7min-95% B, 9 min- 95% B, 10min-1% B, 14 min- 1% B.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:0min-1% B, 1min-15%B, 4min-35% B, 7min-95% B, 9 min- 95% B, 10min-1% B, 14 min- 1% B
Flow Rate:300µL/min
Solvent A:100% water; 0.1%formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003095
Analysis ID:AN003325
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization (ESI) source was operated for both positive mode (+) and negative (-) ionization at 120,000 resolution in MS1 mode and 30000 resolution in data-dependent MS2 scan mode. The spray voltage used for these positive and negative modes is 4000 and 35000 volts respectively. Sheath gas and auxiliary gas were set to 42 and 11 respectively. The mass scan range was 60-900 m/z, ACG (Automatic control gain) target at 100000 ions and maximum injection time was 50 ms for MS and ACG target was 20000 ions and maximum injection time 60 ms for MSMS was used. Data were processed using the IDSL.IPA software (https://cran.r-project.org/web/packages/IDSL.IPA/index.html)
Ion Mode:POSITIVE
  
MS ID:MS003096
Analysis ID:AN003326
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization (ESI) source was operated for both positive mode (+) and negative (-) ionization at 120,000 resolution in MS1 mode and 30000 resolution in data-dependent MS2 scan mode. The spray voltage used for these positive and negative modes is 4000 and 35000 volts respectively. Sheath gas and auxiliary gas were set to 42 and 11 respectively. The mass scan range was 60-900 m/z, ACG (Automatic control gain) target at 100000 ions and maximum injection time was 50 ms for MS and ACG target was 20000 ions and maximum injection time 60 ms for MSMS was used. Data were processed using the IDSL.IPA software (https://cran.r-project.org/web/packages/IDSL.IPA/index.html)
Ion Mode:NEGATIVE
  
MS ID:MS003097
Analysis ID:AN003327
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization (ESI) source was operated for both positive mode (+) and negative (-) ionization at 120,000 resolution in MS1 mode and 30000 resolution in data-dependent MS2 scan mode. The spray voltage used for these positive and negative modes is 4000 and 35000 volts respectively. Sheath gas and auxiliary gas were set to 42 and 11 respectively. The mass scan range was 60-900 m/z, ACG (Automatic control gain) target at 100000 ions and maximum injection time was 50 ms for MS and ACG target was 20000 ions and maximum injection time 60 ms for MSMS was used. Data were processed using the IDSL.IPA software (https://cran.r-project.org/web/packages/IDSL.IPA/index.html)
Ion Mode:POSITIVE
  
MS ID:MS003098
Analysis ID:AN003328
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The electrospray ionization (ESI) source was operated for both positive mode (+) and negative (-) ionization at 120,000 resolution in MS1 mode and 30000 resolution in data-dependent MS2 scan mode. The spray voltage used for these positive and negative modes is 4000 and 35000 volts respectively. Sheath gas and auxiliary gas were set to 42 and 11 respectively. The mass scan range was 60-900 m/z, ACG (Automatic control gain) target at 100000 ions and maximum injection time was 50 ms for MS and ACG target was 20000 ions and maximum injection time 60 ms for MSMS was used. Data were processed using the IDSL.IPA software (https://cran.r-project.org/web/packages/IDSL.IPA/index.html)
Ion Mode:NEGATIVE
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