Summary of Study ST001200
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 PR000808. The data can be accessed directly via it's Project DOI: 10.21228/M87M3D 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 | ST001200 |
| Study Title | Biological Responses to Tobacco Smoke Exposure in III Children: Inflammatory Processes and the Oral Microbiome |
| Study Summary | This project evaluates the biological response to overall tobacco smoke (OTS) exposure among pediatric emergency patients enrolled in a randomized-controlled intervention trial aimed at reducing secondhand smoke exposure. The effects of OTS as measured by salivary continine on salivary metabolic profiles are measured by untargeted high resolution metabolomics, comparing higher and lower levels of OTS. |
| Institute | Emory University |
| Department | School of Medicine |
| Laboratory | Clincal Biomarkers Laboratory |
| Last Name | Uppal |
| First Name | Karan |
| Address | NA |
| kuppal2@emory.edu | |
| Phone | (404) 727 5027 |
| Submit Date | 2019-06-12 |
| Total Subjects | 284 |
| Study Comments | Both CHEAR pooled saliva samples and Clinical Biomarker Laboratory pooled plasma samples were used |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML, raw(Thermo) |
| Chear Study | 2017-1762 |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-05-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000808 |
| Project DOI: | doi: 10.21228/M87M3D |
| Project Title: | Biological Responses to Tobacco Smoke Exposure in III Children: Inflammatory Processes and the Oral Microbiome |
| Project Type: | NIH/NIEHS 1U2CES026560-01 |
| Project Summary: | This project evaluates the biological response to overall tobacco smoke (OTS) exposure among pediatric emergency patients enrolled in a randomized-controlled intervention trial aimed at reducing secondhand smoke exposure. The effects of OTS as measured by salivary continine on salivary metabolic profiles are measured by untargeted high resolution metabolomics, comparing higher and lower levels of OTS. |
| Institute: | Emory University |
| Department: | School of Medicine |
| Laboratory: | Clinical Biomarkers Laboratory |
| Last Name: | Tran |
| First Name: | ViLinh |
| Address: | NA |
| Email: | vtran6@emory.edu |
| Phone: | (404) 727 5027 |
| Funding Source: | NIEHS ES026560 |
Subject:
| Subject ID: | SU001267 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | Ages 0 to 17 years |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Plasma |
|---|---|---|
| SA083514 | Q-Std Plasma pool_5c_1 | Plasma |
| SA083515 | Q-Std Plasma pool_3e_1 | Plasma |
| SA083516 | Q-Std Plasma pool_5d_1 | Plasma |
| SA083517 | Q-Std Plasma pool_7b_1 | Plasma |
| SA083518 | Q-Std Plasma pool_7a_1 | Plasma |
| SA083519 | Q-Std Plasma pool_2a_1 | Plasma |
| SA083520 | Q-Std Plasma pool_6f_1 | Plasma |
| SA083521 | Q-Std Plasma pool_3f_1 | Plasma |
| SA083522 | Q-Std Plasma pool_4b_1 | Plasma |
| SA083523 | Q-Std Plasma pool_7c_1 | Plasma |
| SA083524 | Q-Std Plasma pool_4a_1 | Plasma |
| SA083525 | Q-Std Plasma pool_1e_1 | Plasma |
| SA083526 | Q-Std Plasma pool_1f_1 | Plasma |
| SA083527 | Q-Std Plasma pool_6e_1 | Plasma |
| SA083528 | Q-Std Plasma pool_2d_1 | Plasma |
| SA083529 | Q-Std Plasma pool_6b_1 | Plasma |
| SA083530 | Q-Std Plasma pool_6a_1 | Plasma |
| SA083531 | Q-Std Plasma pool_2e_1 | Plasma |
| SA083532 | Q-Std Plasma pool_2f_1 | Plasma |
| SA083533 | Q-Std Plasma pool_3b_1 | Plasma |
| SA083534 | Q-Std Plasma pool_3a_1 | Plasma |
| SA083535 | Q-Std Plasma pool_6c_1 | Plasma |
| SA083536 | Q-Std Plasma pool_6d_1 | Plasma |
| SA083537 | Q-Std Plasma pool_3d_1 | Plasma |
| SA083538 | Q-Std Plasma pool_7d_1 | Plasma |
| SA083539 | Q-Std Plasma pool_3c_1 | Plasma |
| SA083540 | Q-Std Plasma pool_5e_1 | Plasma |
| SA083541 | Q-Std Plasma pool_5f_1 | Plasma |
| SA083542 | Q-Std Plasma pool_2c_1 | Plasma |
| SA083543 | Q-Std Plasma pool_2b_1 | Plasma |
| SA083544 | Q-Std Plasma pool_5a_1 | Plasma |
| SA083545 | Q-Std Plasma pool_1c_1 | Plasma |
| SA083546 | Q-Std Plasma pool_1d_1 | Plasma |
| SA083547 | NIST SRM 1950_1a | Plasma |
| SA083548 | Q-Std Plasma pool_4d_1 | Plasma |
| SA083549 | Q-Std Plasma pool_7f_1 | Plasma |
| SA083550 | Q-Std Plasma pool_7e_1 | Plasma |
| SA083551 | NIST SRM 1950_2a | Plasma |
| SA083552 | Q-Std Plasma pool_4f_1 | Plasma |
| SA083553 | Q-Std Plasma pool_4c_1 | Plasma |
| SA083554 | Q-Std Plasma pool_5b_1 | Plasma |
| SA083555 | Q-Std Plasma pool_1a_1 | Plasma |
| SA083556 | Q-Std Plasma pool_1b_1 | Plasma |
| SA083557 | Q-Std Plasma pool_4e_1 | Plasma |
| SA083558 | C-1GNU8-SL-01_2 | Saliva |
| SA083559 | C-1GL68-SL-01_2 | Saliva |
| SA083560 | C-1GNV6-SL-01_2 | Saliva |
| SA083561 | C-1GNN3-SL-01_2 | Saliva |
| SA083562 | C-1GN82-SL-01_2 | Saliva |
| SA083563 | C-1GN74-SL-01_2 | Saliva |
| SA083564 | C-1GN90-SL-01_2 | Saliva |
| SA083565 | C-1GNE3-SL-01_2 | Saliva |
| SA083566 | C-1GNM6-SL-01_2 | Saliva |
| SA083567 | C-1GNL8-SL-01_2 | Saliva |
| SA083568 | C-1GL76-SL-01_2 | Saliva |
| SA083569 | salivapool_5e_1 | Saliva |
| SA083570 | C-1GPC6-SL-01_2 | Saliva |
| SA083571 | C-1GKX4-SL-01_2 | Saliva |
| SA083572 | C-1GP98-SL-01_2 | Saliva |
| SA083573 | C-1GPD3-SL-01_2 | Saliva |
| SA083574 | C-1GPG7-SL-01_2 | Saliva |
| SA083575 | C-1GPK8-SL-01_2 | Saliva |
| SA083576 | C-1GPJ0-SL-01_2 | Saliva |
| SA083577 | C-1GP64-SL-01_2 | Saliva |
| SA083578 | salivapool_6b_1 | Saliva |
| SA083579 | C-1GN41-SL-01_2 | Saliva |
| SA083580 | C-1GL27-SL-01_2 | Saliva |
| SA083581 | C-1GL35-SL-01_2 | Saliva |
| SA083582 | C-1GL19-SL-01_2 | Saliva |
| SA083583 | salivapool_5f_1 | Saliva |
| SA083584 | salivapool_6a_1 | Saliva |
| SA083585 | C-1GKY2-SL-01_2 | Saliva |
| SA083586 | C-1GP07-SL-01_2 | Saliva |
| SA083587 | C-1GN09-SL-01_2 | Saliva |
| SA083588 | C-SZJH5-SL-01_2 | Saliva |
| SA083589 | C-1GMD6-SL-01_2 | Saliva |
| SA083590 | C-1GMC9-SL-01_2 | Saliva |
| SA083591 | C-1GMH8-SL-01_2 | Saliva |
| SA083592 | C-1GMJ3-SL-01_2 | Saliva |
| SA083593 | C-1GL92-SL-01_2 | Saliva |
| SA083594 | C-1GLA4-SL-01_2 | Saliva |
| SA083595 | C-1GM91-SL-01_2 | Saliva |
| SA083596 | C-1GM67-SL-01_2 | Saliva |
| SA083597 | C-1GLF3-SL-01_2 | Saliva |
| SA083598 | C-1GLT2-SL-01_2 | Saliva |
| SA083599 | C-1GLS4-SL-01_2 | Saliva |
| SA083600 | C-1GLD7-SL-01_2 | Saliva |
| SA083601 | C-1GLV8-SL-01_2 | Saliva |
| SA083602 | C-1GLW6-SL-01_2 | Saliva |
| SA083603 | C-QDNY3-SL-01_2 | Saliva |
| SA083604 | C-1GMK1-SL-01_2 | Saliva |
| SA083605 | C-1GML9-SL-01_2 | Saliva |
| SA083606 | C-1GMV7-SL-01_2 | Saliva |
| SA083607 | salivapool_4e_1 | Saliva |
| SA083608 | salivapool_4f_1 | Saliva |
| SA083609 | C-1GMX2-SL-01_2 | Saliva |
| SA083610 | C-1GLG1-SL-01_2 | Saliva |
| SA083611 | C-1GN25-SL-01_2 | Saliva |
| SA083612 | C-1GN17-SL-01_2 | Saliva |
| SA083613 | C-1GMR6-SL-01_2 | Saliva |
Collection:
| Collection ID: | CO001261 |
| Collection Summary: | Saliva samples were collected from participants in the randomized controlled trial, An Intervention to Reduce Secondhand Smoke Exposure among Pediatric Emergency Patients, at baseline and a six-week follow up visit. Saliva samples were collected at baseline and a six-week follow up visit by standard protocol using oral swab collection, centrifugation and aliquots trasnferred to 1.8ml freezer tubes and stored in a -70 degree C freezer. The samples were shipped on dry ice from the Cincinnati Children's Hospital Medical Center biorepository storage facility and subsequently to the metabolomics analysis lab at Emory University. |
| Sample Type: | plasma |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001282 |
| Treatment Summary: | Samples were received frozen in aliquouts of <250uL. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section. |
Sample Preparation:
| Sampleprep ID: | SP001275 |
| 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 eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, urine was equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (14,000 rpm 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). |
| Sampleprep Protocol ID: | HRM_SP_082016_01 |
| Sampleprep Protocol Filename: | EmoryUniversity_HRM_SP_082016_01.pdf |
| Sampleprep Protocol Comments: | Date effective: 30 July 2016 |
| Extraction Method: | 2:1 acetonitrile: sample followed by vortexing and centrifugation |
Combined analysis:
| Analysis ID | AN001996 | AN001997 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard | Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005 |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH001444 |
| Chromatography Summary: | The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 microliters of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C. |
| Methods ID: | 2% formic acid in LC-MS grade water |
| Methods Filename: | 20160920_posHILIC120kres5min_ESI_c18negwash.meth |
| Chromatography Comments: | Triplicate injections for each chromatography mode |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard |
| Column Temperature: | 60 C |
| Sample Injection: | 10 uL |
| Solvent A: | 100% water |
| Solvent B: | 100% acetonitrile |
| Analytical Time: | 5 min |
| Sample Loop Size: | 15 uL |
| Sample Syringe Size: | 100 uL |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001445 |
| Chromatography Summary: | The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6- port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min. |
| Methods ID: | 10mM ammonium acetate in LC-MS grade water |
| Methods Filename: | 20160920_negC18120kres5min_ESI_HILICposwash.meth |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005 |
| Column Temperature: | 60C |
| Flow Rate: | 0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min |
| Sample Injection: | 10 uL |
| Solvent A: | 100% water |
| Solvent B: | 100% acetonitrile |
| Analytical Time: | 5 min |
| Sample Loop Size: | 15 uL |
| Sample Syringe Size: | 100 uL |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001849 |
| Analysis ID: | AN001996 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | NA |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 250C |
| Collision Gas: | N2 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 150C |
| Mass Accuracy: | < 3ppm |
| Spray Voltage: | 3500 |
| Activation Parameter: | 5.00E+05 |
| Activation Time: | 118ms |
| Interface Voltage: | S-Lens RF level= 55 |
| Scanning Range: | 85-1275 |
| Analysis Protocol File: | EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf |
| MS ID: | MS001850 |
| Analysis ID: | AN001997 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | NA |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 250C |
| Collision Gas: | N2 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 150C |
| Mass Accuracy: | < 3ppm |
| Spray Voltage: | -4000 |
| Activation Parameter: | 5.00E+05 |
| Activation Time: | 118ms |
| Interface Voltage: | S-Lens RF level= 55 |
| Scanning Range: | 85-1275 |
| Analysis Protocol File: | EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf |
