Summary of Study ST002798

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 IDST002798
Study TitleEvaluation of quantitative performance with serial dilutions
Study TypeUntargeted Metabolomics
Study SummaryTo benchmark the quantitative performance of MetaboAnalystR, a dilution series was prepared by mixing serum and urine in a cross-gradient manner (0:100, 1:1024, 1:256, 1:64, 1:16, 1:4, 1:1, 4:1, 16:1, 64:1, 256:1, 1024:1, 100:0).
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 Date2023-07-26
Num Groups13
Total Subjects1
Num Males1
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

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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:SU002905
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:22-32
Gender:Male

Factors:

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

mb_sample_id local_sample_id Mode Ratio
SA300486SA_01_C18negC18 Negative 0;100
SA300487SA_03_C18negC18 Negative 0;100
SA300488SA_02_C18negC18 Negative 0;100
SA300489SM_03_C18negC18 Negative 100;0
SA300490SM_01_C18negC18 Negative 100;0
SA300491SM_02_C18negC18 Negative 100;0
SA300492SL_03_C18negC18 Negative 1024;1
SA300493SL_02_C18negC18 Negative 1024;1
SA300494SL_01_C18negC18 Negative 1024;1
SA30049820220406_URINE_NonTargetDDMS2_SCAN04_NEGATIVE_RPLCC18 Negative 1;1
SA30049920220406_URINE_NonTargetDDMS2_SCAN03_NEGATIVE_RPLCC18 Negative 1;1
SA30050020220406_URINE_NonTargetDDMS2_SCAN02_NEGATIVE_RPLCC18 Negative 1;1
SA30050120220406_URINE_NonTargetDDMS2_SCAN01_NEGATIVE_RPLCC18 Negative 1;1
SA30050220220406_URINE_NonTargetDDMS2_SCAN05_NEGATIVE_RPLCC18 Negative 1;1
SA300503URINEDDA2_C18negC18 Negative 1;1
SA300504URINEDIA2_1_C18negC18 Negative 1;1
SA300505URINEDIA1_C18negC18 Negative 1;1
SA300506URINEDIA2_C18negC18 Negative 1;1
SA300507URINEDIA3_1_C18negC18 Negative 1;1
SA300508URINEDIA3_C18negC18 Negative 1;1
SA300509URINEDIA1_1_C18negC18 Negative 1;1
SA30051020220406_URINE_DIA_02_NEGATIVE_RPLCC18 Negative 1;1
SA300511URINEDDA2_1_C18negC18 Negative 1;1
SA300512URINEDDA1_C18negC18 Negative 1;1
SA300513URINEDDA3_1_C18negC18 Negative 1;1
SA300514URINEDDA3_C18negC18 Negative 1;1
SA30051520220406_URINE_DIA_01_NEGATIVE_RPLCC18 Negative 1;1
SA30051620220406_URINE_NonTargetDDMS2_SCAN06_NEGATIVE_RPLCC18 Negative 1;1
SA300517URINEDDA1_1_C18negC18 Negative 1;1
SA300518SG_02_C18negC18 Negative 1;1
SA300519SG_03_C18negC18 Negative 1;1
SA300520SG_01_C18negC18 Negative 1;1
SA300521SB_01_C18negC18 Negative 1;1024
SA300522SB_02_C18negC18 Negative 1;1024
SA300523SB_03_C18negC18 Negative 1;1024
SA300524SE_03_C18negC18 Negative 1;16
SA300525SE_01_C18negC18 Negative 1;16
SA300526SE_02_C18negC18 Negative 1;16
SA300527SC_01_C18negC18 Negative 1;256
SA300528SC_02_C18negC18 Negative 1;256
SA300529SC_03_C18negC18 Negative 1;256
SA300530SF_01_C18negC18 Negative 1;4
SA300531SF_02_C18negC18 Negative 1;4
SA300532SF_03_C18negC18 Negative 1;4
SA300495SI_02_C18negC18 Negative 16;1
SA300496SI_01_C18negC18 Negative 16;1
SA300497SI_03_C18negC18 Negative 16;1
SA300533SD_01_C18negC18 Negative 1;64
SA300534SD_03_C18negC18 Negative 1;64
SA300535SD_02_C18negC18 Negative 1;64
SA300536SK_02_C18negC18 Negative 256;1
SA300537SK_01_C18negC18 Negative 256;1
SA300538SK_03_C18negC18 Negative 256;1
SA300539SH_02_C18negC18 Negative 4;1
SA300540SH_03_C18negC18 Negative 4;1
SA300541SH_01_C18negC18 Negative 4;1
SA300542SJ_01_C18negC18 Negative 64;1
SA300543SJ_02_C18negC18 Negative 64;1
SA300544SJ_03_C18negC18 Negative 64;1
SA300545SA_03_C18posC18 Positive 0;100
SA300546SA_02_C18posC18 Positive 0;100
SA300547SA_01_C18posC18 Positive 0;100
SA300548SM_03_C18posC18 Positive 100;0
SA300549SM_02_C18posC18 Positive 100;0
SA300550SM_01_C18posC18 Positive 100;0
SA300551SL_02_C18posC18 Positive 1024;1
SA300552SL_03_C18posC18 Positive 1024;1
SA300553SL_01_C18posC18 Positive 1024;1
SA30055720220406_URINE_NonTargetDDMS2_SCAN04_POSITIVE_RPLCC18 Positive 1;1
SA30055820220406_URINE_NonTargetDDMS2_SCAN05_POSITIVE_RPLCC18 Positive 1;1
SA30055920220406_URINE_NonTargetDDMS2_SCAN02_POSITIVE_RPLCC18 Positive 1;1
SA30056020220406_URINE_NonTargetDDMS2_SCAN01_POSITIVE_RPLCC18 Positive 1;1
SA30056120220406_URINE_NonTargetDDMS2_SCAN03_POSITIVE_RPLCC18 Positive 1;1
SA300562URINEDDA1_C18posC18 Positive 1;1
SA300563URINEDIA2_1_C18posC18 Positive 1;1
SA300564URINEDIA1_C18posC18 Positive 1;1
SA300565URINEDIA2_C18posC18 Positive 1;1
SA300566URINEDIA3_1_C18posC18 Positive 1;1
SA300567URINEDIA3_C18posC18 Positive 1;1
SA300568URINEDIA1_1_C18posC18 Positive 1;1
SA30056920220406_URINE_DIA_02_POSITIVE_RPLCC18 Positive 1;1
SA300570URINEDDA2_1_C18posC18 Positive 1;1
SA300571URINEDDA1_1_C18posC18 Positive 1;1
SA300572URINEDDA2_C18posC18 Positive 1;1
SA300573URINEDDA3_1_C18posC18 Positive 1;1
SA300574URINEDDA3_C18posC18 Positive 1;1
SA30057520220406_URINE_NonTargetDDMS2_SCAN06_POSITIVE_RPLCC18 Positive 1;1
SA30057620220406_URINE_DIA_01_POSITIVE_RPLCC18 Positive 1;1
SA300577SG_01_C18posC18 Positive 1;1
SA300578SG_02_C18posC18 Positive 1;1
SA300579SG_03_C18posC18 Positive 1;1
SA300580SB_03_C18posC18 Positive 1;1024
SA300581SB_01_C18posC18 Positive 1;1024
SA300582SB_02_C18posC18 Positive 1;1024
SA300583SE_02_C18posC18 Positive 1;16
SA300584SE_01_C18posC18 Positive 1;16
SA300585SE_03_C18posC18 Positive 1;16
SA300586SC_03_C18posC18 Positive 1;256
SA300587SC_02_C18posC18 Positive 1;256
SA300588SC_01_C18posC18 Positive 1;256
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 220

Collection:

Collection ID:CO002898
Collection Summary:serum standards and an urine sample is mixed based on a series of dilution ratio
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002914
Treatment Summary:Healthy volunteers were recruited. About 1 mL urine were collected. The urine sample was mixed with a serum sample then. No other treatment applied.

Sample Preparation:

Sampleprep ID:SP002911
Sampleprep Summary:A urine sample was collected from a donor of McGill University45. A total of 100mL urine was sub-sampled and frozen at -80°C. A human standard serum sample (Sigma-Aldrich, Sigma, St. Louis, MO, USA) and the urine were thawed in ice for 1 hour, and then vortexed for 30 seconds to ensure homogeneity. A total of 13 Eppendorf microcentrifuge tubes were prepared and labelled from A to M. For tubes A to E, 150 µl urine was transferred into each of them. For tube G to K, 150 µl standard serum was transferred into each of them. 250 µl pure urine were transferred into tube L, and 250 µl pure serum were transferred into tube M. Then, 50 µl pure serum were extracted and mixed into tube E. Then, 50 µl liquids were extracted and mixed into tube D, and so on until tube A. Same operations were repeated for pure urine tube L, and tube G-K. Finally, 75 µl pure urine and serum were extracted respectively and mixed into tube F. At a result, a total of 11 dilution mixtures and 2 pure samples were generated.
Processing Storage Conditions:On ice
Extraction Method:Organic reagent
Extract Storage:On ice

Combined analysis:

Analysis ID AN004552 AN004553
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:CH003420
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:CH003421
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:MS004299
Analysis ID:AN004552
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:MS004300
Analysis ID:AN004553
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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