Description
Biomedical Resilience & Readiness in Adverse Operating Environments (BRAVE) Project: Exhaled Breath Condensate (EBC) TMT Proteomic Transformation Data
Exhaled breath condensate (EBC) represents a low-cost and non-invasive means of examining respiratory health. EBC has been used to discover and validate exhaled volatile and non-volatile biomarkers of disease related to the respiratory system distress such as asthma, COPD, lung cancer, and secondary infections. One newly emerging utilization of EBC, is proteomics analysis, which can provide an unbiased snapshot into ongoing biological processes in the airway. Fully characterizing the biological landscape of EBC collections is challenging though, due to sample variability, and low detection sensitivity. EBC is primarily composed of condensed water, causing technical challenges with detecting key macromolecules from the dilute sample matrix; therefore, high sensitivity techniques are required to unlock the full capability of EBC as a method for non-invasive biomarker detection. To overcome some of these technical challenges for proteomic analyses, we applied our recently developed microscale proteomic techniques and developed a novel TMT-tag approach enabling reliable, relative quantification with significantly improved detection of low abundance peptides/proteins across multiple healthy volunteer EBC samples. Our EBC collection design includes longitudinal EBC collections from five individual healthy volunteers on three separate days of the week with triplicate, back-to-back donations each day. This work will pave the way for further investigations of EBC protein expression profiles and showcase the value of using non-invasive collection method techniques for clinically relevant biomarker discovery.
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Reusable FAIRsharing Project Selected Repository Standards
Proteomic Mass Spectrometry Data Collections:
Primary Data Archive
- PRIDE: 10.25504/FAIRsharing.e1byny (reusable formats: raw, mzML, xml)
Secondary Data Archive
- PNNL DataHub: 10.17616/R31NJN56 (reusable formats: csv, fasta)
Accessible Secondary Data Downloads
Download contains normalized dataset abundance values. Quantification data was prepared using novel microscale proteomic isobaric labeling tandem mass tag (TMT-tag MS) techniques from samples collected from a small cohort of healthy human volunteers (M/F) in a longitudinal study.
- BRAVE_EBC-TMT.1.0.csv (processed TMT proteomic data)
- H_sapiens_UniProt_SPROT_2019-02-22.fasta (protein collection file; UniProt Proteome: UP000005640)
- BRAVE_EBC-TMT.1.0_OSTI.GOV-metadata.json (OSTI dataset DOI registration metadata)
Linked Open Primary Data Downloads
Raw measurement capability data have been deposited at community recognized public database(s) where appropriate and are the recorded factual material accepted by the scientific community necessary to validate the resulting publication of information consistent with intellectual property provisions under which the publishable information was produced. See standard file formats from HUPO-PSI found at the PRoteomics IDEntifications database (PRIDE) on how to report peptide/protein identification and quantification results.
- PRIDE Accession: PXD021763
Acknowledgments
This research was supported by the LDRD Biomedical Resilience And Readiness in AdVerse Operating Environments (BRAVE) Project (73748), and was conducted at Pacific Northwest National Laboratory (PNNL) in Richland, WA. PNNL is a multiprogram national laboratory operated by Battelle for the Department of Energy (DOE) under Contract DE-AC05-76RLO 1830. A portion of this project work was performed on instrument capabilities operating under the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility, sponsored by the Biological and Environmental Research program operating under Contract No. DE-AC05-76RL01830.
Data Reuse
Recommendation guidelines provided by the DOE Office of Science can be accessed at the SC Funding Opportunities & Acknowledgements homepage. For additional information regarding user capability data release and reuse, visit the SC Digital Data Management Resources at User Facilities for more information.
Cite as: Anderson, Lindsey N, Piehowski, Paul D, Hutchinson-Bunch, Chelsea, Carnley, Yessica, Wang, Yang, & Teeguarden, Justin. BRAVE_EBC-TMT.1.0. United States. doi: 10.25584/BraveEBC/1769003. url: https://data.pnnl.gov/group/nodes/dataset/13426.
Last updated on 2022-10-19T16:43:27+00:00 by LN Anderson
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