Summary of Study ST002454

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 PR001582. The data can be accessed directly via it's Project DOI: 10.21228/M86Q7N 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 IDST002454
Study TitleBloody Mary (BM21)- Serial mixtures of vegetable juice /water and human plasma.
Study SummaryMetabolomics holds the promise to measure and quantify small molecules comprehensively in biological systems, and LC-MS (liquid chromatography coupled mass spectrometry) has become the leading technology in the field. Significant challenges still exist in the computational processing of data from LC-MS metabolomic experiments into metabolite features, including provenance and reproducibility of the current software tools. We present here, an experiment designed as serial mixtures of vegetable juice/Water and human plasma at varying ratios, nicknamed “Bloody Mary 21(BM21) to test semi-quantification at –omics scale. A subset of features are expected to have their peak areas correlated with the mixing ratio. This dataset provides an opportunity to be used as benchmark to assess the performance in quantification of processing softwares. Overall, the BM21 experiment included a serial mixture of human plasma (Qstd) and vegetable juice (or water), at the ratio of 1024:1, 256:1, 64:1, 16:1, 4:1, 1:1, 1:4, 1:16, 1:64, 1:256 and 1:1024. Along with the 11 serial mixture samples, 100% vegetable juice and 100% plasma were also included. All samples were analyzed in triplicates.
Institute
The Jackson Laboratory for Genomic Medicine
LaboratoryShuzhao Li Lab
Last NameSiddiqa
First NameAmnah
Address10 Discovery Dr, Farmington, CT 06032
Emailamnah.siddiqa@jax.org
Phone404-9187223
Submit Date2022-06-27
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-02-01
Release Version1
Amnah Siddiqa Amnah Siddiqa
https://dx.doi.org/10.21228/M86Q7N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001582
Project DOI:doi: 10.21228/M86Q7N
Project Title:Bloody Mary (BM21)- Serial mixtures of vegetable juice/water and human plasma.
Project Summary:Metabolomics holds the promise to measure and quantify small molecules comprehensively in biological systems, and LC-MS (liquid chromatography coupled mass spectrometry) has become the leading technology in the field. Significant challenges still exist in the computational processing of data from LC-MS metabolomic experiments into metabolite features, including provenance and reproducibility of the current software tools. We present here, an experiment designed as serial mixtures of vegetable juice/Water and human plasma at varying ratios, nicknamed “Bloody Mary 21(BM21) to test semi-quantification at –omics scale. A subset of features are expected to have their peak areas correlated with the mixing ratio. This dataset provides an opportunity to be used as benchmark to assess the performance in quantification of processing softwares.
Institute:The Jackson Laboratory for Genomic Medicine
Laboratory:Shuzhao Li Lab
Last Name:Siddiqa
First Name:Amnah
Address:10 Discovery Dr, Farmington, CT 06032
Email:amnah.siddiqa@jax.org
Phone:4049187223

Subject:

Subject ID:SU002543
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 Factor_Dilutionseries
SA245474Blank_20211013_001Blank
SA245475Blank_20211013_006_20211019161707Blank
SA245476Blank_20211013_004Blank
SA245477Blank_20211020_003Blank
SA245478Blank_20211020_002Blank
SA245479Blank_20211020_006Blank
SA245480Blank_20211020_004Blank
SA245481Blank_20211013_002Blank
SA245482Blank_20211020_005Blank
SA245483Blank_20211020_001Blank
SA245484Blank_20211013_003Blank
SA245485Blank_20211013_005_20211019161135Blank
SA245486Blank_std_20211020_1_001Blank_Std
SA245487Blank_std_20211013_1_002Blank_Std
SA245488Blank_std_20211020_1_002Blank_Std
SA245489Blank_std_20211013_1_001Blank_Std
SA245490MT_20211013_082Pooled
SA245491MT_20211013_048Pooled
SA245492MT_20211013_006Pooled
SA245493MT_20211013_005Pooled
SA245494MT_20211020_082Pooled
SA245495MT_20211020_048Pooled
SA245496MT_20211013_081Pooled
SA245497MT_20211020_081Pooled
SA245498MT_20211020_047Pooled
SA245499MT_20211020_006Pooled
SA245500MT_20211020_005Pooled
SA245501MT_20211013_047Pooled
SA245502MT_20211020_004QC
SA245503MT_20211020_001QC
SA245504MT_20211013_084QC
SA245505MT_20211013_002QC
SA245506MT_20211013_004QC
SA245507MT_20211020_002QC
SA245508MT_20211013_003QC
SA245509MT_20211020_003QC
SA245510MT_20211013_083QC
SA245511MT_20211013_001QC
SA245512MT_20211020_083QC
SA245513MT_20211020_084QC
SA245514MT_20211020_009Qstd;H2O(0;1)_rep1
SA245515MT_20211020_010Qstd;H2O(0;1)_rep1
SA245516MT_20211020_074Qstd;H2O(1024;1)_rep1
SA245517MT_20211020_073Qstd;H2O(1024;1)_rep1
SA245518MT_20211020_076Qstd;H2O(1024;1)_rep2
SA245519MT_20211020_075Qstd;H2O(1024;1)_rep2
SA245520MT_20211020_077Qstd;H2O(1024;1)_rep3
SA245521MT_20211020_078Qstd;H2O(1024;1)_rep3
SA245528MT_20211020_079Qstd;H2O(1;0)_rep1
SA245529MT_20211020_080Qstd;H2O(1;0)_rep1
SA245536MT_20211020_012Qstd;H2O(1;1024)_rep1
SA245537MT_20211020_011Qstd;H2O(1;1024)_rep1
SA245538MT_20211020_014Qstd;H2O(1;1024)_rep2
SA245539MT_20211020_013Qstd;H2O(1;1024)_rep2
SA245540MT_20211020_015Qstd;H2O(1;1024)_rep3
SA245541MT_20211020_016Qstd;H2O(1;1024)_rep3
SA245542MT_20211020_030Qstd;H2O(1;16)_rep1
SA245543MT_20211020_029Qstd;H2O(1;16)_rep1
SA245544MT_20211020_031Qstd;H2O(1;16)_rep2
SA245545MT_20211020_032Qstd;H2O(1;16)_rep2
SA245546MT_20211020_033Qstd;H2O(1;16)_rep3
SA245547MT_20211020_034Qstd;H2O(1;16)_rep3
SA245530MT_20211020_042Qstd;H2O(1;1)_rep1
SA245531MT_20211020_041Qstd;H2O(1;1)_rep1
SA245532MT_20211020_043Qstd;H2O(1;1)_rep2
SA245533MT_20211020_044Qstd;H2O(1;1)_rep2
SA245534MT_20211020_045Qstd;H2O(1;1)_rep3
SA245535MT_20211020_046Qstd;H2O(1;1)_rep3
SA245548MT_20211020_018Qstd;H2O(1;256)_rep1
SA245549MT_20211020_017Qstd;H2O(1;256)_rep1
SA245550MT_20211020_020Qstd;H2O(1;256)_rep2
SA245551MT_20211020_019Qstd;H2O(1;256)_rep2
SA245552MT_20211020_022Qstd;H2O(1;256)_rep3
SA245553MT_20211020_021Qstd;H2O(1;256)_rep3
SA245554MT_20211020_035Qstd;H2O(1;4)_rep1
SA245555MT_20211020_036Qstd;H2O(1;4)_rep1
SA245556MT_20211020_038Qstd;H2O(1;4)_rep2
SA245557MT_20211020_037Qstd;H2O(1;4)_rep2
SA245558MT_20211020_039Qstd;H2O(1;4)_rep3
SA245559MT_20211020_040Qstd;H2O(1;4)_rep3
SA245522MT_20211020_056Qstd;H2O(16;1)_rep1
SA245523MT_20211020_055Qstd;H2O(16;1)_rep1
SA245524MT_20211020_058Qstd;H2O(16;1)_rep2
SA245525MT_20211020_057Qstd;H2O(16;1)_rep2
SA245526MT_20211020_060Qstd;H2O(16;1)_rep3
SA245527MT_20211020_059Qstd;H2O(16;1)_rep3
SA245560MT_20211020_023Qstd;H2O(1;64)_rep1
SA245561MT_20211020_024Qstd;H2O(1;64)_rep1
SA245562MT_20211020_026Qstd;H2O(1;64)_rep2
SA245563MT_20211020_025Qstd;H2O(1;64)_rep2
SA245564MT_20211020_028Qstd;H2O(1;64)_rep3
SA245565MT_20211020_027Qstd;H2O(1;64)_rep3
SA245566MT_20211020_068Qstd;H2O(256;1)_rep1
SA245567MT_20211020_067Qstd;H2O(256;1)_rep1
SA245568MT_20211020_070Qstd;H2O(256;1)_rep2
SA245569MT_20211020_069Qstd;H2O(256;1)_rep2
SA245570MT_20211020_072Qstd;H2O(256;1)_rep3
SA245571MT_20211020_071Qstd;H2O(256;1)_rep3
SA245572MT_20211020_049Qstd;H2O(4;1)_rep1
SA245573MT_20211020_050Qstd;H2O(4;1)_rep1
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 180

Collection:

Collection ID:CO002536
Collection Summary:Vegetable juice and Commercially Pooled Plasma Sample used.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002555
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP002549
Sampleprep Summary:A stepwise dilution (Serial dilution) of vegetable juice and standard pooled human plasma (Qstd) in the opposite direction was used for sample preparation process. Samples were prepared using vegetable juice and Qstd in the ratio of 1024:1, 256:1, 64:1, 16:1, 4:1, 1:1, 1:4, 1:16, 1:64, 1:256 and 1:1024. Along with the 11 serial dilution samples, 100% vegetable juice and 100% plasma were also included as samples. All samples were used in triplicates. Metabolites extraction were carried out by protein precipitation technique using extraction solvent, acetonitrile:methanol (8:1, v/v) containing 0.1% formic acid and isotope labelled Trimethyl-13C3]-caffeine, [13C5]-L-glutamic acid, [15N2]-Uracil, [15N,13C5]-L-methionine, [13C6]-D-glucose and [15N]-L-tyrosine as spike-in controls. 30 ul of Qstd was taken and 60 ul of extraction solvent was added. Extraction blanks were also prepared to remove features of non-biological origins. All samples were vortexed and incubated with shaking at 1000 rpm for 10 min at 4 ºC followed by centrifugation at 4 ºC for 15 min at 15,000 rpm. The supernatant was transferred into mass spec vials and 2 ul injected into UHPLC-MS.

Combined analysis:

Analysis ID AN004003 AN004004
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Accucore 150 Amide (50 x 2.1mm, 2.6um) Thermo Hypersil GOLD (50 x 2.1mm, 3um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE
Units m/z values m/z values

Chromatography:

Chromatography ID:CH002956
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore 150 Amide (50 x 2.1mm, 2.6um)
Column Temperature:45
Flow Gradient:0.55 ml/min: 0-0.1 min: 0% B, 0.10-5.0 min: 98% B, and 5 min for cleaning and equilibration of column.
Flow Rate:0.55 ml/min
Solvent A:95% acetonitrile/5% water; 0.1% acetic acid; 10 mM ammonium acetate
Solvent B:50% acetonitrile/50% water; 0.1% acetic acid; 10 mM ammonium acetate
Chromatography Type:HILIC
  
Chromatography ID:CH002957
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD (50 x 2.1mm, 3um)
Column Temperature:45
Flow Gradient:0-0.1 min: 0% B, 0.10-1.9 min: 60% B, 1.9-5.0 min: 98% B, and 5 min cleaning and column equilibration
Flow Rate:0.4 ml/min
Solvent A:10 mM ammonium acetate in acetonitrile:water (95:5, v/v) with 0.1% acetic acid
Solvent B:10 mM ammonium acetate in acetonitrile:water (95:5, v/v) with 0.1% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003751
Analysis ID:AN004003
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:data processing using asari v1.9.2
Ion Mode:POSITIVE
  
MS ID:MS003752
Analysis ID:AN004004
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:data processing using asari v1.9.2
Ion Mode:NEGATIVE
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