PXD029800-1
PXD029800 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Identification of Endogenous Peptides in MALDI-TOF-MS based COVID-19 diagnostics |
| Description | Mass spectrometry (MS) based diagnostic detection of 2019 novel coronavirus infectious disease (COVID19) has been postulated to be a useful alternative to classical PCR based diagnostics. These MS based approaches have the potential to be both rapid, sensitive and can be done onsite without requiring a dedicated laboratory or depending on constrained supply chains (i.e., reagents and consumables). Matrix Assisted Laser Desorption Ionization (MALDI) time of flight (TOF) MS, has a long and established history of microorganism detection. Previously, we have shown that automated machine learning (ML) enhanced MALDI TOF MS diagnostics of nasal swabs can be both sensitive and specific for COVID19 detection. The underlying molecules responsible for this detection are generally unknown nor required for this automated ML platform to detect COVID19. However, the identification of these molecules is important for both understanding the diagnostic test itself and potentially the biology of the underlying infection. Here, we used nanoscale liquid chromatography tandem MS to identify endogenous peptides found in COVID19 positive anterior nares swab saline transport media to characterize mass over charge (m/z) values observed by the MALDI TOF MS method. We identified 14,270 endogenous peptides across 1,245 proteins groups that primarily comprise poly immunoglobulin receptor, actin, statherin, glyceraldehyde3phosphate dehydrogenase, basic salivary prolinerich protein 1 and histones. We also show that SARSCoV2 viral peptides were not readily detected and are highly unlikely to be responsible for the accuracy of MALDI based SARSCoV2 diagnostics. |
| HostingRepository | MassIVE |
| AnnounceDate | 2022-05-05 |
| AnnouncementXML | Submission_2022-05-05_11:17:45.186.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Brett Phinney |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Deamidated |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2021-11-18 14:46:06 | ID requested | |
| ⏵ 1 | 2022-05-05 11:17:45 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: COVID-19 |
Contact List
| Nam K. Tran | |
|---|---|
| contact affiliation | Department of Pathology and Laboratory Medicine University of California Davis |
| contact email | nktran@ucdavis.edu |
| lab head | |
| Brett Phinney | |
| contact affiliation | UC Davis |
| contact email | brettsp@ucdavis.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000088411/ |
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