Summary of Study ST001132

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 PR000757. The data can be accessed directly via it's Project DOI: 10.21228/M8TQ2B 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 IDST001132
Study TitleInvestigate the False Discovery in Biomarker Research Using LC-HRMS based Untargeted Metabolomics Profiling
Study Typemimicking metabolomics study
Study SummaryPooled human plasma was spiked separately with two different sets of 11 metabolite standards (22 “true biomarkers”) to mimic plasma samples collected from diseased subjects and non-diseased subjects. Metabolite extracts of individual samples were subjected to biomarker discovery using LC-HRMS.
Institute
University of Macau
DepartmentInstitute of Translational Medicine - Faculty of Health Sciences
LaboratoryPilot Laboratory
Last NameZhang
First NamePW
AddressTaipa
Emailyb47620@um.edu.mo
Phone88222534
Submit Date2019-02-05
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2020-03-03
Release Version1
PW Zhang PW Zhang
https://dx.doi.org/10.21228/M8TQ2B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000757
Project DOI:doi: 10.21228/M8TQ2B
Project Title:Investigate the False Discovery in Biomarker Research Using LC-HRMS based Untargeted Metabolomics Profiling
Project Summary:Pooled human plasma was spiked separately with two different sets of 11 metabolite standards (22 “true biomarkers”) to mimic plasma samples collected from diseased subjects and non-diseased subjects. Metabolite extracts of individual samples were subjected to biomarker discovery using LC-HRMS.
Institute:University of Macau
Department:Institute of Translational Medicine - Faculty of Health Sciences
Laboratory:Pilot Laboratory
Last Name:Zhang
First Name:PW
Address:Taipa
Email:yb47620@um.edu.mo
Phone:88222534
Funding Source:University of Macau

Subject:

Subject ID:SU001193
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Pooled
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id SampleType
SA078118Blank1blank
SA078119Blank2blank
SA078120Negative control13no treatment
SA078121Negative control14no treatment
SA078122Negative control15no treatment
SA078123Negative control12no treatment
SA078124Negative control11no treatment
SA078125Negative control9no treatment
SA078126Negative control10no treatment
SA078127Negative control16no treatment
SA078128Negative control24no treatment
SA078129Negative control22no treatment
SA078130Negative control23no treatment
SA078131Negative control8no treatment
SA078132Negative control21no treatment
SA078133Negative control20no treatment
SA078134Negative control18no treatment
SA078135Negative control19no treatment
SA078136Negative control17no treatment
SA078137Negative control7no treatment
SA078138Negative control3no treatment
SA078139Negative control1no treatment
SA078140Negative control4no treatment
SA078141Negative control2no treatment
SA078142Negative control5no treatment
SA078143Negative control6no treatment
SA078107QC4QC
SA078108QC6QC
SA078109QC3QC
SA078110QC2QC
SA078111QC1QC
SA078112QC7QC
SA078113QC5QC
SA078114QC11QC
SA078115QC10QC
SA078116QC8QC
SA078117QC9QC
SA078144A1spiked SetA
SA078145A8spiked SetA
SA078146A9spiked SetA
SA078147A11spiked SetA
SA078148A7spiked SetA
SA078149A10spiked SetA
SA078150A3spiked SetA
SA078151A2spiked SetA
SA078152A12spiked SetA
SA078153A4spiked SetA
SA078154A5spiked SetA
SA078155A6spiked SetA
SA078156B5spiked SetB
SA078157B9spiked SetB
SA078158B10spiked SetB
SA078159B11spiked SetB
SA078160B12spiked SetB
SA078161B8spiked SetB
SA078162B7spiked SetB
SA078163B2spiked SetB
SA078164B3spiked SetB
SA078165B4spiked SetB
SA078166B6spiked SetB
SA078167B1spiked SetB
Showing results 1 to 61 of 61

Collection:

Collection ID:CO001187
Collection Summary:Pooled human potassium EDTA plasma was purchased from a commercial company (Equitech-Bio Inc., Kerrville, TX, USA)
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001208
Treatment Summary:Mimicking diseased plasma samples and non-diseased samples (12 samples for each group) were spiked with Set A and Set B metabolite standards, respectively. Two groups of negative control samples (12 samples for each group) were also prepared, but replacing Set A and Set B metabolite standard mixtures with LC-MS grade water. Information of the two sets of metabolite standards spiked into the human pooled plasma. Set A (metabolite standard spiked concentration μM): L-Leucine 250,Creatine 110, L-Histidine 160, L-Phenylalanine 130, D-(+)-Glucose 10000, L-Aspartic Acid 40, L-Valine 460, L-Alanine 660, L-Serine 280, L-Carnitine 90, L-Glutamine 1180. Set B (metabolite standard spiked concentration μM): Creatinine 150, L-Proline 480, Betaine 150, L-Glycine 460, L-Arginine 220, L-Threonine 280, L-Tryptophan 100, L-Lysine 360, L-Glutamic Acid 170, L-Asparagine 80, Hypoxanthine 20.

Sample Preparation:

Sampleprep ID:SP001201
Sampleprep Summary:1. Preparation of Metabolite Standard Spiked Plasma Samples for the Biomarker Discovery Experiment Individual metabolite standard solutions were prepared in LC-MS grade water. Each set of metabolite standards was prepared separately by mixing equal volumes of 11 metabolite standards. The two metabolite mixtures was dried by speed vacuum at room temperature, and redissolved separately in the human pooled plasma to form two master spiked plasma samples. Each of the two master spiked plasma samples was divided into 12 identical aliquots (each 30 µL), which were treated as plasma samples collected from 12 different people. The quality control (QC) sample was prepared by mixing equal amount of solutions of each spiked plasma sample, and it was used to check the stability of the system throughout the sequence analysis. 2. Preparation of Plasma Samples for the Negative Control Experiment Two groups of negative control samples (12 identical samples for each group) were prepared according to the above strategy, but replacing Set A and Set B metabolite standard mixtures with LC-MS grade water. 3. Preparation of Blank Sample The solvent extraction blank samples were prepared according to the plasma metabolite extraction procedure, but replacing plasma with equal volume of MS grade water. 4. Plasma Metabolite Extraction Frozen pooled plasma samples were thawed at 4 oC and vortexed for 30 seconds before metabolite extraction. Thirty microliters of plasma were mixed with 120 µL chilled methanol, and vortexed for 30 seconds. The mixture was incubated at 4 oC for 20 minutes to precipitate the proteins. After incubation, the mixture was centrifuged at 14,000 g for 10 min to pellet the proteins. The supernatant were recovered as the metabolite extract, and stored at -80 oC before LC-HRMS analysis.
Processing Storage Conditions:4℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN001857
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Unspecified
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units ARBITRARY

Chromatography:

Chromatography ID:CH001344
Chromatography Summary:Individual metabolite extracts were separated on an amide HILIC (Accucore™ 150 Amide HILIC 2.1×150 mm, Thermo Fisher) column at a flow rate of 0.3 mL/min using a UHPLC system (Dionex UltiMate 3000, Thermo Fisher).The optimized stepwise linear gradient:10% B in the first 2 min, 10% - 30% B in the next 5 min, followed by 30% - 60% in 3 min, and finally 60% - 90% in 5 min.
Methods Filename:Chromatography
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Unspecified
Column Temperature:30
Flow Rate:0.3 ml/min
Injection Temperature:8
Sample Injection:2 micro litter
Solvent A:98% acetonitrile/2% water; 0.1% formic acid
Solvent B:98% water/2% acetonitrile; 0.1% formic acid; 30 mM ammonium formate
Analytical Time:21 min
Capillary Voltage:320
Preconditioning:1h
Chromatography Type:HILIC

MS:

MS ID:MS001717
Analysis ID:AN001857
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:spray voltage, 3.5 kV; capillary temperature, 320 °C; sheath gas flow rate, 45; auxiliary gas flow rate, 25; heater temperature 350 °C; AGC, 3×106; maximum injection time, 200 ms; mass scan range, 50–750; full MS resolution, 70,000 FWHM at m/z 200; spectrum data type, profile.
Ion Mode:POSITIVE
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