PXD055483-1

PXD055483 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	QCeltis Case Study 2: Native Plasma QC Dataset
Description	A dataset containing native plasma samples used as quality control digestion replicates. Samples were automatically processed on i7 automated liquid handling system (Beckman Coulter). Briefly, proteins were extracted and denatured with a buffer composed of TFE (2,2,2-Trifluoroethanol), DTT and ammonium bicarbonate prior being alkylated, reduced and digested with trypsin. Obtained tryptic peptides were desalted by SPE (Solid Phase Extraction) on C18 stationary phase. Pooled whole blood and plasma samples were used as digestion control replicates (DRs). 5 DRs were added to each digestion plate to be digested with the cohort data. DIA-MS analysis was performed on an Orbitrap Exploris 480 (Thermo Fisher) instrument using MS-MS settings with tryptic peptides separated by EVOSEP One LC System (Evosep) over a 60-minute gradient. During LC-MS acquisition, the 5 DRs are run at the beginning of each batch.
HostingRepository	MassIVE
AnnounceDate	2025-06-23
AnnouncementXML	Submission_2025-06-23_12:34:10.356.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manasa Vegesna
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-02 13:34:34	ID requested
⏵ 1	2025-06-23 12:34:11	announced

Publication List

Vegesna M, Sundararaman N, Bharadwaj A, Washington K, Pandey R, Haghani A, Chazarin B, Binek A, Fu Q, Cheng S, Herrington D, Van Eyk JE, . J Proteome Res, 24(3):1148-1160(2025) [pubmed]

Vegesna M, Sundararaman N, Bharadwaj A, Washington K, Pandey R, Haghani A, Chazarin B, Binek A, Fu Q, Cheng S, Herrington D, Van Eyk JE, . J Proteome Res, 24(3):1148-1160(2025) [pubmed]

Keyword List

submitter keyword: DIA, Quality Control, Digestion Replicates, Native Plasma

submitter keyword: DIA, Quality Control, Digestion Replicates, Native Plasma

Contact List

Jennifer Van Eyk
contact affiliation	Cedars Sinai Medical Center
contact email	jennifer.vaneyk@cshs.org
lab head
Manasa Vegesna
contact affiliation	Cedars-Sinai Medical Center
contact email	manasa.vegesna@cshs.org
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-ftp.ucsd.edu/v08/MSV000095744/

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-ftp.ucsd.edu/v08/MSV000095744/