NIST SRM Smoker non-Smoker Urine Comparison
Ontology highlight
ABSTRACT:
INSTRUMENT(S): GC x GC-TOF
ORGANISM(S): Human Homo Sapiens
TISSUE(S): Urine
SUBMITTER: 
Jason Burgess
PROVIDER: ST000420 | MetabolomicsWorkbench | Fri Jun 10 00:00:00 BST 2016
REPOSITORIES: MetabolomicsWorkbench
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| mwtab | Other |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Six biological samples including the cell, feces, plasma (NIST SRM 1950), tissue, urine, and their pooled sample were analyzed by UPLC-HRMS.
2022-04-22 | MSV000089300 | MassIVE
Project description:This metabolomics projects was to evaluate the differences between pooled urine from smokers and non-smokers from NIST.
2016-06-13 | ST000411 | MetabolomicsWorkbench
Project description:Six biological samples including the cell, feces, plasma (NIST SRM 1950), tissue, urine, and their pooled sample were analyzed by UPLC-HRMS.
2022-04-22 | MSV000089300 | GNPS
Project description:W evaluated an experimental particle exposure model, including markers of the acute phase system assessed as the hepatic mRNA expression of Sap, the murine homologue of CRP, and Saa1 and Saa3. Experiment Overall Design: 12-13 weeks old Apoe knockout mice (C57BL/6-Apoe tm1) mice were injected intraperitoneally with varying doses of SRM 2975. In a parallel experiment C57BL mice were exposed by inhalation for 90 minutes to four consecutive doses of 20mg/m3 of filtered air, NIST 2975 or Ptintex 90. Livers and aortic tissue were collected.
2009-05-02 | E-GEOD-11346 | biostudies-arrayexpress
Project description:Proper QA/QC is an essential component of any analytical procedure. The variability in platforms and approaches used by the untargeted cores requires that each lab develop specific QA/QC protocols, making cross-laboratory assessments challenging. To address the difference in measures across the untargeted cores, the untargeted quality assurance working group (UQAWG) has identified the importance of using the same biological reference sample across the different laboratories. To reach this goal, Dr. Jones and Mr. Walker of Emory University volunteered to take the lead in identifying vendors, requesting quotes, purchasing the pooled material, delivering the specified volumes to each of the lab hubs and storing additional material on-site at Emory University. Based upon discussion with the UQAWG, it was decided that each participating laboratory (five total) will receive 500 mL of plasma and 2000 mL of urine, providing sufficient volume for daily analysis over the next five years. Initially, NIST standard reference materials were considered; however, limited supply and cost makes the use of NIST materials impractical. Vendors, including BioreclamationIVT, Lee Biosolutions Inc and Gemini Bio-Products were contacted to request quotes for preparing pooled plasma and urine meeting the following requirements: K2EDTA recovered whole blood (plasma), equal distribution male/female, equal distribution of Black/Hispanic/Caucasian donors and be collected from greater than 40 donors. In addition, we requested all blood samples be collected in FDA inspected facilities, provide collection details, provide general demographics for each donor and be delivered in 500 mL aliquots. BioreclamationIVT, who also provided the biological samples for the NIH metabolomics ring trial, was selected as the most appropriate vendor due to the ability to provide the requested materials, lead-time to deliver and price. To date, both pools have been purchased. The urine pool was received on July 21, 2016 and the plasma pool will be received July 26, 2016. Upon receipt, both pools will be stored at -80°C. Summary demographics were provided by BioreclamationIVT, the urine pool was created by combining urine samples from 60 males and 60 females with an average age of 38 (range 18-60) and equal distribution of races. The plasma pool was created by combining recovered plasma obtained from 50 males and 50 females with an average age of 38.4 (range 19-72) and equal distribution of races. Both urine and plasma pools will be delivered to the lab hubs frozen in units of 500 mL. Upon receipt, plasma and urine pools should be aliquoted into volumes that provide sufficient material so that freeze-thaw of the pooled material is minimized. For unambiguous identification, the urine pool has been named UrineRef_20160721 and the plasma pool has been named PlasmaRef_20160726. The purpose of providing each untargeted lab hub with the pooled material is two-fold. Through analysis of UrineRef_20160721 (if study samples are urine) or PlasmaRef_20160726 (if study samples are plasma) in each batch of samples analyzed for CHEAR, it will be possible to have a common reference across the different lab hubs. Thus, the ability to compare analyses on different platforms will be greatly improved. The use of a consistent reference material in each batch will also facilitate reference standardization, a concept developed for retrospective quantification of high-resolution metabolomics (Go, Walker et al. 2015). Using reference standardization, quantification post-data acquisition is possible by referencing the pooled material analyzed with each series of samples. The pooled material can be characterized and analytes quantified using traditional analytical chemistry techniques, such as quantification by methods of addition or standardization with a certified reference material, such as NIST SRM 1950. Known concentrations within the pooled material can be used to determine an analyte response factor and calculate sample concentrations based on single-point calibration. The benefit of this approach is that targeted quantification is only required in the pooled sample (i.e. UrineRef_20160721 or PlasmaRef_20160726), chemicals selected for quantification do not need to be selected a priori, and population wide estimates of plasma chemical concentrations can be determined without having to re-analyze samples using a targeted approach. Current Clinical Biomarker Laboratory protocol requires three analytical replicates of pooled reference material per day (three technical replicates per analytical replicate per column configuration, or 18 injections/instrument-day), resulting in analyses of the reference material every 10 samples. Results from untargeted LC-HRMS analyses of pooled CHEAR reference materials. PlasmaRef_20160726 was analyzed with additional NIST reference materials: SRM 1950, SRM 1957 and SRM 1958. UrineRef_20160721 was analyzed with NIST reference materials SRM 3672 and 3673.
2017-02-17 | ST000596 | MetabolomicsWorkbench
Project description:Proper QA/QC is an essential component of any analytical procedure. The variability in platforms and approaches used by the untargeted cores requires that each lab develop specific QA/QC protocols, making cross-laboratory assessments challenging. To address the difference in measures across the untargeted cores, the untargeted quality assurance working group (UQAWG) has identified the importance of using the same biological reference sample across the different laboratories. To reach this goal, Dr. Jones and Mr. Walker of Emory University volunteered to take the lead in identifying vendors, requesting quotes, purchasing the pooled material, delivering the specified volumes to each of the lab hubs and storing additional material on-site at Emory University. Based upon discussion with the UQAWG, it was decided that each participating laboratory (five total) will receive 500 mL of plasma and 2000 mL of urine, providing sufficient volume for daily analysis over the next five years. Initially, NIST standard reference materials were considered; however, limited supply and cost makes the use of NIST materials impractical. Vendors, including BioreclamationIVT, Lee Biosolutions Inc and Gemini Bio-Products were contacted to request quotes for preparing pooled plasma and urine meeting the following requirements: K2EDTA recovered whole blood (plasma), equal distribution male/female, equal distribution of Black/Hispanic/Caucasian donors and be collected from greater than 40 donors. In addition, we requested all blood samples be collected in FDA inspected facilities, provide collection details, provide general demographics for each donor and be delivered in 500 mL aliquots. BioreclamationIVT, who also provided the biological samples for the NIH metabolomics ring trial, was selected as the most appropriate vendor due to the ability to provide the requested materials, lead-time to deliver and price. To date, both pools have been purchased. The urine pool was received on July 21, 2016 and the plasma pool will be received July 26, 2016. Upon receipt, both pools will be stored at -80°C. Summary demographics were provided by BioreclamationIVT, the urine pool was created by combining urine samples from 60 males and 60 females with an average age of 38 (range 18-60) and equal distribution of races. The plasma pool was created by combining recovered plasma obtained from 50 males and 50 females with an average age of 38.4 (range 19-72) and equal distribution of races. Both urine and plasma pools will be delivered to the lab hubs frozen in units of 500 mL. Upon receipt, plasma and urine pools should be aliquoted into volumes that provide sufficient material so that freeze-thaw of the pooled material is minimized. For unambiguous identification, the urine pool has been named UrineRef_20160721 and the plasma pool has been named PlasmaRef_20160726. The purpose of providing each untargeted lab hub with the pooled material is two-fold. Through analysis of UrineRef_20160721 (if study samples are urine) or PlasmaRef_20160726 (if study samples are plasma) in each batch of samples analyzed for CHEAR, it will be possible to have a common reference across the different lab hubs. Thus, the ability to compare analyses on different platforms will be greatly improved. The use of a consistent reference material in each batch will also facilitate reference standardization, a concept developed for retrospective quantification of high-resolution metabolomics (Go, Walker et al. 2015). Using reference standardization, quantification post-data acquisition is possible by referencing the pooled material analyzed with each series of samples. The pooled material can be characterized and analytes quantified using traditional analytical chemistry techniques, such as quantification by methods of addition or standardization with a certified reference material, such as NIST SRM 1950. Known concentrations within the pooled material can be used to determine an analyte response factor and calculate sample concentrations based on single-point calibration. The benefit of this approach is that targeted quantification is only required in the pooled sample (i.e. UrineRef_20160721 or PlasmaRef_20160726), chemicals selected for quantification do not need to be selected a priori, and population wide estimates of plasma chemical concentrations can be determined without having to re-analyze samples using a targeted approach. Current Clinical Biomarker Laboratory protocol requires three analytical replicates of pooled reference material per day (three technical replicates per analytical replicate per column configuration, or 18 injections/instrument-day), resulting in analyses of the reference material every 10 samples. Results from untargeted LC-HRMS analyses of pooled CHEAR reference materials. PlasmaRef_20160726 was analyzed with additional NIST reference materials: SRM 1950, SRM 1957 and SRM 1958. UrineRef_20160721 was analyzed with NIST reference materials SRM 3672 and 3673.
2017-02-21 | ST000595 | MetabolomicsWorkbench
Project description:This dataset contains lipidomics data of NIST SRM 1950 plasma acquired by the three-fold approach: capillary LC/nanoelectrospray for enhanced ionization, QLT for higher sensitivity, and maximized parallelization of mass analyzers for efficient acquisition.
2022-01-27 | MSV000088741 | MassIVE
Project description:mRNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer
2011-06-01 | GSE29006 | GEO
Project description:Background: Healthy individuals exposed to low levels of cigarette smoke have a decrement in lung function and higher risk for lung disease compared to unexposed individuals. We hypothesized that healthy individuals exposed to low levels of tobacco smoke must have biologic changes in the small airway epithelium compared to healthy unexposed individuals. Methods: Small airway epithelium was obtained by bronchoscopy from 121 individuals; microarrays assessed genome wide gene expression, and urine nicotine and cotinine were used to categorized subjects as “nonsmokers,” “active smokers,” and “low exposure.” The gene expression data was used to determine the threshold and ID50 of urine nicotine and cotinine at which the small airway epithelium showed abnormal responses. Results: There was no threshold of urine nicotine without an abnormal small airway epithelial response, and only a slightly above detectable threshold abnormal response for cotinine. The nicotine ID50 for nicotine was 25 ng/ml and cotinine 104 ng/ml. Conclusions: The small airway epithelium detects and responds to low levels of tobacco smoke with transcriptome modifications. This provides biologic correlates of epidemiologic studies linking low level tobacco smoke exposure to lung health risk, health, identifies genes in the lung cells most sensitive to tobacco smoke and defines thresholds at the lung epithelium responds to inhaled tobacco smoke. Affymetrix arrays were used to assess the gene expression data of smoking-responsive genes in the in small airway epithelium obtained by fiberoptic bronchoscopy of 48 healthy non-smokers (non-smoker or Nsaets), 65 healthy smokers (smoker), 7 symptomatic smokers (SYMs) and a healthy occasional smoker (OcSs). YSB and LO contributed equally to the study.
2011-02-02 | E-GEOD-19667 | biostudies-arrayexpress
Project description:A technical comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits, by triplicate sequencing of the cell line DNA of NA12878, NA12891, NA12892 and NIST RM8395
2019-09-20 | E-MTAB-8349 | biostudies-arrayexpress