Summary of Study ST001161

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 PR000777. The data can be accessed directly via it's Project DOI: 10.21228/M87T23 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 IDST001161
Study TitleEvaluation of computational tools using serial mixtures of human plasma and vegetable juice (part-I)
Study SummaryMass spectrometry-based metabolomics is developed rapidly in the past few decades. There are few major vendors for LC-MS platform instruments, for example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass spectrometer were used for metabolomics research. The data acquired cross different platform are rarely compared other than the comparison of the instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan speed etc., which is largely due to the foundation and principle of the instrument design. Other than this, there are many choice for data preprocessing, i.e., the data acquired from the same platform may have been processed with different feature extraction software tools. The discrepancy for the feature detections with different software will lead to the variation of the down-stream statistics analysis and metabolomics pathway interpretation. In addition, the impact of the LC-MS platform and data preprocessing software tools on the quantitative capabilities is also an interesting topic. In this research, XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF LC-MS platform by serial dilution experiment. The quantification capability is estimated at the same time based on the linearity, accuracy, and precision
Institute
Emory University
Last NameWang
First NameYating
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emailyating.wang@emory.edu
Phone4047275091
Submit Date2019-03-29
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-05-15
Release Version1
Yating Wang Yating Wang
https://dx.doi.org/10.21228/M87T23
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000777
Project DOI:doi: 10.21228/M87T23
Project Title:Evaluation of computational tools using serial mixtures of human plasma and vegetable juice
Project Summary:Mass spectrometry-based metabolomics is developed rapidly in the past few decades. There are few major vendors for LC-MS platform instruments, for example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass spectrometer were used for metabolomics research. The data acquired cross different platform are rarely compared other than the comparison of the instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan speed etc., which is largely due to the foundation and principle of the instrument design. Other than this, there are many choice for data preprocessing, i.e., the data acquired from the same platform may have been processed with different feature extraction software tools. The discrepancy for the feature detections with different software will lead to the variation of the down-stream statistics analysis and metabolomics pathway interpretation. In addition, the impact of the LC-MS platform and data preprocessing software tools on the quantitative capabilities is also an interesting topic. In this research, XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF LC-MS platform by serial dilution experiment. The quantification capability is estimated at the same time based on the linearity, accuracy, and precision
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarker Laboratory
Last Name:Wang
First Name:Yating
Address:615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Email:yating.wang@emory.edu
Phone:4047275091

Subject:

Subject ID:SU001226
Subject Type:Other
Subject Species:Homo sapiens
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Sample.Composition
SA0804620-1_100v8food
SA0804630-9_1_16_vqfood and human plasma
SA0804640-10_1_64_vqfood and human plasma
SA0804650-11_1_256_vqfood and human plasma
SA0804660-12_1_1024_vqfood and human plasma
SA0804670-8_1_4_vqfood and human plasma
SA0804680-7_1_1_vqfood and human plasma
SA0804690-2_1024_1_vqfood and human plasma
SA0804700-3_256_1_vqfood and human plasma
SA0804710-4_64_1_vqfood and human plasma
SA0804720-6_4_1_vqfood and human plasma
SA0804730-5_16_1_vqfood and human plasma
SA0804740-13_100q3human plasma
Showing results 1 to 13 of 13

Collection:

Collection ID:CO001220
Collection Summary:Commecially available
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001241
Treatment Summary:Samples were prepared by mixing commercially available vegetable juice and human plsama Qstandard. Smaples were mixed in the ratio of vegetable jucie to plasma at 1024:1, 256:1,64:1, 16:1, 4:1, 1:1, 1:4, 1:16, 1:256, 1:1024. Prior to analysis, samples were stored in -80 degree C.

Sample Preparation:

Sampleprep ID:SP001234
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods(Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80 degrees C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 microliters was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 microliters of ice-cold LC-MS grade acetonitrile(Sigma Aldrich) containing 2.5 microliters of internal standard solution with eleven stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, samples were equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (14,000rpm at 4 degrees C for 10 min). The resulting supernatant (100 microliters) was removed, added to a low volume autosampler vial and maintained at 4 degrees C until analysis (<22 h).

Combined analysis:

Analysis ID AN001919 AN001920
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo ScientificTM LTQ Orbitrap Velos Thermo ScientificTM LTQ Orbitrap Velos
Column Waters XBridge Amide (100 x 4.6mm,3.5um) Thermo Accucore C18 (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo LTQ Orbitrap Velos Thermo Velos LTQ Orbitrap
Ion Mode POSITIVE POSITIVE
Units Peak Area Peak Area

Chromatography:

Chromatography ID:CH001392
Instrument Name:Thermo ScientificTM LTQ Orbitrap Velos
Column Name:Waters XBridge Amide (100 x 4.6mm,3.5um)
Chromatography Type:HILIC
  
Chromatography ID:CH001393
Instrument Name:Thermo ScientificTM LTQ Orbitrap Velos
Column Name:Thermo Accucore C18 (100 x 2.1mm,2.6um)
Chromatography Type:Reversed phase

MS:

MS ID:MS001775
Analysis ID:AN001919
Instrument Name:Thermo LTQ Orbitrap Velos
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Convert to mzXML format using MSConvert; XCMS R package was used to extract feature table
Ion Mode:POSITIVE
  
MS ID:MS001776
Analysis ID:AN001920
Instrument Name:Thermo Velos LTQ Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Convert to mzXML format using MSConvert; XCMS R package was used to extract feature table
Ion Mode:POSITIVE
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