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.
Study ID | ST002798 |
Study Title | Evaluation of quantitative performance with serial dilutions |
Study Type | Untargeted Metabolomics |
Study Summary | To 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 |
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 |
jeff.xia@mcgill.ca | |
Phone | 5143988668 |
Submit Date | 2023-07-26 |
Num Groups | 13 |
Total Subjects | 1 |
Num Males | 1 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2024-01-01 |
Release Version | 1 |
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: | SU002905 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 22-32 |
Gender: | Male |
Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Mode | Ratio |
---|---|---|---|
SA300486 | SA_01_C18neg | C18 Negative | 0;100 |
SA300487 | SA_03_C18neg | C18 Negative | 0;100 |
SA300488 | SA_02_C18neg | C18 Negative | 0;100 |
SA300489 | SM_03_C18neg | C18 Negative | 100;0 |
SA300490 | SM_01_C18neg | C18 Negative | 100;0 |
SA300491 | SM_02_C18neg | C18 Negative | 100;0 |
SA300492 | SL_03_C18neg | C18 Negative | 1024;1 |
SA300493 | SL_02_C18neg | C18 Negative | 1024;1 |
SA300494 | SL_01_C18neg | C18 Negative | 1024;1 |
SA300498 | 20220406_URINE_NonTargetDDMS2_SCAN04_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300499 | 20220406_URINE_NonTargetDDMS2_SCAN03_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300500 | 20220406_URINE_NonTargetDDMS2_SCAN02_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300501 | 20220406_URINE_NonTargetDDMS2_SCAN01_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300502 | 20220406_URINE_NonTargetDDMS2_SCAN05_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300503 | URINEDDA2_C18neg | C18 Negative | 1;1 |
SA300504 | URINEDIA2_1_C18neg | C18 Negative | 1;1 |
SA300505 | URINEDIA1_C18neg | C18 Negative | 1;1 |
SA300506 | URINEDIA2_C18neg | C18 Negative | 1;1 |
SA300507 | URINEDIA3_1_C18neg | C18 Negative | 1;1 |
SA300508 | URINEDIA3_C18neg | C18 Negative | 1;1 |
SA300509 | URINEDIA1_1_C18neg | C18 Negative | 1;1 |
SA300510 | 20220406_URINE_DIA_02_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300511 | URINEDDA2_1_C18neg | C18 Negative | 1;1 |
SA300512 | URINEDDA1_C18neg | C18 Negative | 1;1 |
SA300513 | URINEDDA3_1_C18neg | C18 Negative | 1;1 |
SA300514 | URINEDDA3_C18neg | C18 Negative | 1;1 |
SA300515 | 20220406_URINE_DIA_01_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300516 | 20220406_URINE_NonTargetDDMS2_SCAN06_NEGATIVE_RPLC | C18 Negative | 1;1 |
SA300517 | URINEDDA1_1_C18neg | C18 Negative | 1;1 |
SA300518 | SG_02_C18neg | C18 Negative | 1;1 |
SA300519 | SG_03_C18neg | C18 Negative | 1;1 |
SA300520 | SG_01_C18neg | C18 Negative | 1;1 |
SA300521 | SB_01_C18neg | C18 Negative | 1;1024 |
SA300522 | SB_02_C18neg | C18 Negative | 1;1024 |
SA300523 | SB_03_C18neg | C18 Negative | 1;1024 |
SA300524 | SE_03_C18neg | C18 Negative | 1;16 |
SA300525 | SE_01_C18neg | C18 Negative | 1;16 |
SA300526 | SE_02_C18neg | C18 Negative | 1;16 |
SA300527 | SC_01_C18neg | C18 Negative | 1;256 |
SA300528 | SC_02_C18neg | C18 Negative | 1;256 |
SA300529 | SC_03_C18neg | C18 Negative | 1;256 |
SA300530 | SF_01_C18neg | C18 Negative | 1;4 |
SA300531 | SF_02_C18neg | C18 Negative | 1;4 |
SA300532 | SF_03_C18neg | C18 Negative | 1;4 |
SA300495 | SI_02_C18neg | C18 Negative | 16;1 |
SA300496 | SI_01_C18neg | C18 Negative | 16;1 |
SA300497 | SI_03_C18neg | C18 Negative | 16;1 |
SA300533 | SD_01_C18neg | C18 Negative | 1;64 |
SA300534 | SD_03_C18neg | C18 Negative | 1;64 |
SA300535 | SD_02_C18neg | C18 Negative | 1;64 |
SA300536 | SK_02_C18neg | C18 Negative | 256;1 |
SA300537 | SK_01_C18neg | C18 Negative | 256;1 |
SA300538 | SK_03_C18neg | C18 Negative | 256;1 |
SA300539 | SH_02_C18neg | C18 Negative | 4;1 |
SA300540 | SH_03_C18neg | C18 Negative | 4;1 |
SA300541 | SH_01_C18neg | C18 Negative | 4;1 |
SA300542 | SJ_01_C18neg | C18 Negative | 64;1 |
SA300543 | SJ_02_C18neg | C18 Negative | 64;1 |
SA300544 | SJ_03_C18neg | C18 Negative | 64;1 |
SA300545 | SA_03_C18pos | C18 Positive | 0;100 |
SA300546 | SA_02_C18pos | C18 Positive | 0;100 |
SA300547 | SA_01_C18pos | C18 Positive | 0;100 |
SA300548 | SM_03_C18pos | C18 Positive | 100;0 |
SA300549 | SM_02_C18pos | C18 Positive | 100;0 |
SA300550 | SM_01_C18pos | C18 Positive | 100;0 |
SA300551 | SL_02_C18pos | C18 Positive | 1024;1 |
SA300552 | SL_03_C18pos | C18 Positive | 1024;1 |
SA300553 | SL_01_C18pos | C18 Positive | 1024;1 |
SA300557 | 20220406_URINE_NonTargetDDMS2_SCAN04_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300558 | 20220406_URINE_NonTargetDDMS2_SCAN05_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300559 | 20220406_URINE_NonTargetDDMS2_SCAN02_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300560 | 20220406_URINE_NonTargetDDMS2_SCAN01_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300561 | 20220406_URINE_NonTargetDDMS2_SCAN03_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300562 | URINEDDA1_C18pos | C18 Positive | 1;1 |
SA300563 | URINEDIA2_1_C18pos | C18 Positive | 1;1 |
SA300564 | URINEDIA1_C18pos | C18 Positive | 1;1 |
SA300565 | URINEDIA2_C18pos | C18 Positive | 1;1 |
SA300566 | URINEDIA3_1_C18pos | C18 Positive | 1;1 |
SA300567 | URINEDIA3_C18pos | C18 Positive | 1;1 |
SA300568 | URINEDIA1_1_C18pos | C18 Positive | 1;1 |
SA300569 | 20220406_URINE_DIA_02_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300570 | URINEDDA2_1_C18pos | C18 Positive | 1;1 |
SA300571 | URINEDDA1_1_C18pos | C18 Positive | 1;1 |
SA300572 | URINEDDA2_C18pos | C18 Positive | 1;1 |
SA300573 | URINEDDA3_1_C18pos | C18 Positive | 1;1 |
SA300574 | URINEDDA3_C18pos | C18 Positive | 1;1 |
SA300575 | 20220406_URINE_NonTargetDDMS2_SCAN06_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300576 | 20220406_URINE_DIA_01_POSITIVE_RPLC | C18 Positive | 1;1 |
SA300577 | SG_01_C18pos | C18 Positive | 1;1 |
SA300578 | SG_02_C18pos | C18 Positive | 1;1 |
SA300579 | SG_03_C18pos | C18 Positive | 1;1 |
SA300580 | SB_03_C18pos | C18 Positive | 1;1024 |
SA300581 | SB_01_C18pos | C18 Positive | 1;1024 |
SA300582 | SB_02_C18pos | C18 Positive | 1;1024 |
SA300583 | SE_02_C18pos | C18 Positive | 1;16 |
SA300584 | SE_01_C18pos | C18 Positive | 1;16 |
SA300585 | SE_03_C18pos | C18 Positive | 1;16 |
SA300586 | SC_03_C18pos | C18 Positive | 1;256 |
SA300587 | SC_02_C18pos | C18 Positive | 1;256 |
SA300588 | SC_01_C18pos | C18 Positive | 1;256 |
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 |