PXD025277 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients |
Description | We sought to characterize the host response through proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry and high-resolution QTOF mass spectrometer with a parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of nasopharyngeal swabs was performed in PASEF-DDA mode, which identified 7,723 proteins and 102,392 peptides that were then used for constructing a spectral library. Subsequently, quantitative proteome profiling was carried out for 90 nasopharyngeal swab samples in diaPASEF mode which resulted in 5,023 protein identifications. Functional analysis revealed two significant features of biological processes of innate immune response and viral life cycle. Overall, we provide the in-depth proteome record from nasopharyngeal swab samples and suggest relevant host response along with proteins playing a pivotal role against viral infection, which would assist for mining promising drug targets in the future. |
HostingRepository | PRIDE |
AnnounceDate | 2021-10-08 |
AnnouncementXML | Submission_2021-10-08_04:53:02.671.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Akhilesh Pandey |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-04-08 19:44:00 | ID requested | |
⏵ 1 | 2021-10-08 04:53:03 | announced | |
Publication List
Mun DG, Vanderboom PM, Madugundu AK, Garapati K, Chavan S, Peterson JA, Saraswat M, Pandey A, DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. J Proteome Res, 20(8):4165-4175(2021) [pubmed] |
Keyword List
ProteomeXchange project tag: Sars-cov-2, Covid-19 |
submitter keyword: DIA, timsTOF, COVD-19, host response, nasopharyngeal swabs |
Contact List
Akhilesh Pandey |
contact affiliation | Department of Laboratory Medicine and Pathology & Center for Individualized Medicine Mayo Clinic Rochester MN 55905, USA |
contact email | pandey.akhilesh@mayo.edu |
lab head | |
Akhilesh Pandey |
contact affiliation | Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 |
contact email | pandey.akhilesh@mayo.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025277
- Label: PRIDE project
- Name: DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients