PXD025277

PXD025277 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-08 19:44:00	ID requested
⏵ 1	2021-10-08 04:53:03	announced

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]

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: DIA, timsTOF, COVD-19, host response, nasopharyngeal swabs

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

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://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD025277

PRIDE project URI

• PRIDE
  1. PXD025277
     1. Label: PRIDE project
     2. Name: DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients