Summary of Study ST002796

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 PR001744. The data can be accessed directly via it's Project DOI: 10.21228/M88Q6W 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 IDST002796
Study TitleComparison of different blood samples (whole blood, serum and plasma)
Study TypeUntargeted Metabolomics
Study SummaryTo evaluate the performance of compounds annotation in real biological samples, we conducted LC-MS/MS based metabolomics including both DDA and SWATH-DIA on paired blood samples of different types (plasma, serum and whole blood) and compared their chemical differences.
Institute
McGill University
DepartmentFaculty of Agricultural and Environmental Sciences
LaboratoryXia Lab, Institute of Parasitology
Last NameXia
First NameJeff
AddressMacdonald Campus, McGill University 21,111 Lakeshore Road
Emailjeff.xia@mcgill.ca
Phone5143988668
Submit Date2023-07-25
Num Groups3
Total Subjects14
Num Males7
Num Females7
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-01-01
Release Version1
Jeff Xia Jeff Xia
https://dx.doi.org/10.21228/M88Q6W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001744
Project DOI:doi: 10.21228/M88Q6W
Project Title:MetaboAnalystR 4.0: towards a unified LC-MS workflow for global metabolomics
Project Type:MS/MS qualification and MS quantification study
Project Summary:Here we introduce MetaboAnalystR 4.0, an open-source R package that have been developed to provide a unified workflow to help address three key bioinformatics bottlenecks facing LC-MS-based global metabolomics, including: 1) auto-optimized LC-MS spectral processing for feature detection and quantification; 2) streamlined MS/MS spectral deconvolution and compound annotation coupled with comprehensive spectral reference databases (~1.5 million MS2 spectra); 3) a sensitive functional interpretation module for functional analysis directly from LC-MS and MS/MS results. During our validation case studies in comparison with other well-established approaches, MetaboAnalystR 4.0 has identified > 10% more high-quality MS and MS/MS features; it has also significantly increased true positive rate of identification (> 40%) without increasing false positives using both data-dependent acquisition (DDA) and data-independent acquisition (DIA) datasets; finally, pathway enrichment analysis integrating LC-MS and MS/MS spectra from COVID-19 datasets has produced results that are better aligned with literature report.
Institute:McGill University
Department:Faculty of Agricultural and Environmental Sciences
Laboratory:Xia Lab, Institute of Parasitology
Last Name:Xia
First Name:Jeff
Address:Macdonald Campus, McGill University 21,111 Lakeshore Road
Email:jeff.xia@mcgill.ca
Phone:5146605018
Funding Source:NIH, TIMIC, Genome Canada, Génome Québec
Contributors:Zhiqiang Pang, Lei Xu, Charles Viau

Subject:

Subject ID:SU002903
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:22-32
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Mode Blood_type
SA300180PLASMA12_C18negC18 Negative Plasma
SA300181PLASMA11_C18negC18 Negative Plasma
SA300182PLASMA14_C18negC18 Negative Plasma
SA300183PLASMA15_C18negC18 Negative Plasma
SA300184PLASMA01_C18negC18 Negative Plasma
SA300185PLASMA10_C18negC18 Negative Plasma
SA300186PLASMA13_C18negC18 Negative Plasma
SA300187PLASMA05_C18negC18 Negative Plasma
SA300188PLASMA03_C18negC18 Negative Plasma
SA300189PLASMA09_C18negC18 Negative Plasma
SA300190PLASMA06_C18negC18 Negative Plasma
SA300191PLASMA02_C18negC18 Negative Plasma
SA300192PLASMA07_C18negC18 Negative Plasma
SA300193PLASMA08_C18negC18 Negative Plasma
SA300194QCDIA_02_C18negC18 Negative QC
SA300195QCDIA_03_C18negC18 Negative QC
SA300196WB_SERUM_PLASMA_TargetedDDMSC18_NEG01C18 Negative QC
SA300197QCDIA_01_C18negC18 Negative QC
SA300198QCDDA_SCAN3_01_C18negC18 Negative QC
SA300199QCDDA_SCAN2_01_C18negC18 Negative QC
SA300200QCDDA_SCAN2_02_C18negC18 Negative QC
SA300201WB_SERUM_PLASMA_TargetedDDMSC18_NEG02C18 Negative QC
SA300202QCDDA_SCAN3_02_C18negC18 Negative QC
SA300203WB_SERUM_PLASMA_TargetedDDMSC18_NEGall2C18 Negative QC
SA300204WB_SERUM_PLASMA_TargetedDDMSC18_NEG14C18 Negative QC
SA300205WB_SERUM_PLASMA_TargetedDDMSC18_NEGallC18 Negative QC
SA300206QCDDA_SCAN1_02_C18negC18 Negative QC
SA300207WB_SERUM_PLASMA_TargetedDDMSC18_NEG13C18 Negative QC
SA300208WB_SERUM_PLASMA_TargetedDDMSC18_NEG12C18 Negative QC
SA300209WB_SERUM_PLASMA_TargetedDDMSC18_NEG04C18 Negative QC
SA300210WB_SERUM_PLASMA_TargetedDDMSC18_NEG11C18 Negative QC
SA300211WB_SERUM_PLASMA_TargetedDDMSC18_NEG03C18 Negative QC
SA300212QCDDA_SCAN1_01_C18negC18 Negative QC
SA300213QC5_C18negC18 Negative QC
SA300214QC3_C18negC18 Negative QC
SA300215QC2_C18negC18 Negative QC
SA300216QC1_C18negC18 Negative QC
SA300217QC6_C18negC18 Negative QC
SA300218QC4_C18negC18 Negative QC
SA300219SERUM07_C18negC18 Negative SERUM
SA300220SERUM06_C18negC18 Negative SERUM
SA300221SERUM09_C18negC18 Negative SERUM
SA300222SERUM10_C18negC18 Negative SERUM
SA300223SERUM11_C18negC18 Negative SERUM
SA300224SERUM05_C18negC18 Negative SERUM
SA300225SERUM04_C18negC18 Negative SERUM
SA300226SERUM15_C18negC18 Negative SERUM
SA300227SERUM01_C18negC18 Negative SERUM
SA300228SERUM02_C18negC18 Negative SERUM
SA300229SERUM03_C18negC18 Negative SERUM
SA300230SERUM12_C18negC18 Negative SERUM
SA300231SERUM08_C18negC18 Negative SERUM
SA300232SERUM14_C18negC18 Negative SERUM
SA300233SERUM13_C18negC18 Negative SERUM
SA300234WB04_C18negC18 Negative Whole_Blood
SA300235WB05_C18negC18 Negative Whole_Blood
SA300236WB07_C18negC18 Negative Whole_Blood
SA300237WB03_C18negC18 Negative Whole_Blood
SA300238WB06_C18negC18 Negative Whole_Blood
SA300239WB02_C18negC18 Negative Whole_Blood
SA300240WB09_C18negC18 Negative Whole_Blood
SA300241WB08_C18negC18 Negative Whole_Blood
SA300242WB10_C18negC18 Negative Whole_Blood
SA300243WB01_C18negC18 Negative Whole_Blood
SA300244WB14_C18negC18 Negative Whole_Blood
SA300245WB15_C18negC18 Negative Whole_Blood
SA300246WB13_C18negC18 Negative Whole_Blood
SA300247WB11_C18negC18 Negative Whole_Blood
SA300248WB12_C18negC18 Negative Whole_Blood
SA300249PLASMA12_C18posC18 Positive Plasma
SA300250PLASMA11_C18posC18 Positive Plasma
SA300251PLASMA13_C18posC18 Positive Plasma
SA300252PLASMA15_C18posC18 Positive Plasma
SA300253PLASMA10_C18posC18 Positive Plasma
SA300254PLASMA14_C18posC18 Positive Plasma
SA300255PLASMA02_C18posC18 Positive Plasma
SA300256PLASMA01_C18posC18 Positive Plasma
SA300257PLASMA09_C18posC18 Positive Plasma
SA300258PLASMA05_C18posC18 Positive Plasma
SA300259PLASMA03_C18posC18 Positive Plasma
SA300260PLASMA06_C18posC18 Positive Plasma
SA300261PLASMA07_C18posC18 Positive Plasma
SA300262PLASMA08_C18posC18 Positive Plasma
SA300263QCDIA_01_C18posC18 Positive QC
SA300264QCDIA_03_C18posC18 Positive QC
SA300265QCDDA_SCAN3_02_C18posC18 Positive QC
SA300266QCDIA_02_C18posC18 Positive QC
SA300267QCDDA_SCAN1_02_C18posC18 Positive QC
SA300268WB_SERUM_PLASMA_TargetedDDMSC18_POS01C18 Positive QC
SA300269QCDDA_SCAN2_01_C18posC18 Positive QC
SA300270QCDDA_SCAN2_02_C18posC18 Positive QC
SA300271QCDDA_SCAN3_01_C18posC18 Positive QC
SA300272WB_SERUM_PLASMA_TargetedDDMSC18_POS12C18 Positive QC
SA300273WB_SERUM_PLASMA_TargetedDDMSC18_POS22C18 Positive QC
SA300274WB_SERUM_PLASMA_TargetedDDMSC18_POS23C18 Positive QC
SA300275QCDDA_SCAN1_01_C18posC18 Positive QC
SA300276WB_SERUM_PLASMA_TargetedDDMSC18_POS21C18 Positive QC
SA300277WB_SERUM_PLASMA_TargetedDDMSC18_POS13C18 Positive QC
SA300278WB_SERUM_PLASMA_TargetedDDMSC18_POS03C18 Positive QC
SA300279WB_SERUM_PLASMA_TargetedDDMSC18_POS11C18 Positive QC
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Collection:

Collection ID:CO002896
Collection Summary:Blood samples were collected and processed to gather whole blood, serum and plasma
Sample Type:Blood (whole)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002912
Treatment Summary:Healthy volunteers were recruited. About five milliliters of venous whole blood were drawn from each volunteer into a BD K2-EDTA Trace Element free Vacutainer. No other treatment applied.

Sample Preparation:

Sampleprep ID:SP002909
Sampleprep Summary:The three blood sample types (WB, serum and plasma) were thawed on ice for 1 hour, and then vortexed for 30 seconds to ensure homogeneity. 100 µl of each sample type was transferred to a 1.5 ml Eppendorf microcentrifuge tube, to which 400 µl of -20°C 1:1 ACN:MeOH (v/v) was added. Samples were next vortexed for 60 seconds and stored at -20°C for 1 hour. Samples were then centrifuged at 16,100 × g for 10 minutes at 4°C. The supernatants were collected (250 µl) and filtered by centrifugation using 0.2 µm Nanosep centrifugal filters (PALL Life Sciences) at 14,000 × g for 15 minutes at 4°C. Filtered samples (120 µl) were then transferred to LC-MS vials equipped with 250 µl glass inserts and run in the LC-MS. A Quality Control (QC) sample was made by pooling equal volumes from each filtered all samples supernatant into one 1.5 ml Eppendorf microcentrifuge tube.
Processing Storage Conditions:On ice
Extraction Method:Organic reagent
Extract Storage:On ice

Combined analysis:

Analysis ID AN004548 AN004549
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um) Thermo Accucore HILIC (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE and NEGATIVE POSITIVE and NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH003417
Chromatography Summary:For C18 columns, the composition of the mobile phases A and B were 0.1% FA in water and 0.1% FA in ACN, respectively.
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um)
Column Temperature:40
Flow Gradient:0-1min: 95%A; 1-3min:50%A; 3-15min:20%A; 15-15.5:0%A; 15.5-19.5min: 0%A; 19.5%-20: 95%A
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003418
Chromatography Summary:For HILIC chromatography, the composition of the mobile phases A and B were 50% ACN in water with 5 mmol/L NH4AC and 95% ACN in Water with 5mmol/L NH4AC, respectively.
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore HILIC (100 x 2.1mm,2.6um)
Column Temperature:35
Flow Gradient:0-3min:1%A; 3-20min:50%A; 20-21min: 95%A; 21-24min:95%A; 24-25min:1%A
Flow Rate:0.4 mL/min
Solvent A:50% acetonitrile/50% water; 5 mM ammonium acetate
Solvent B:95% acetonitrile/5% water; 5 mM ammonium acetate
Chromatography Type:HILIC

MS:

MS ID:MS004295
Analysis ID:AN004548
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For the C18 column, an electrospray ion (ESI) source with a spray voltage of 4 keV in positive mode and 3.5 keV in negative mode were used
Ion Mode:POSITIVE and NEGATIVE
  
MS ID:MS004296
Analysis ID:AN004549
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:for HILIC a voltage of 4 keV in positive mode and 3.8 keV in negative mode were used
Ion Mode:POSITIVE and NEGATIVE
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