PXD055481-1

PXD055481 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	QCeltis Case Study 1: Depleted Plasma QC Dataset
Description	A dataset containing depleted plasma samples used as quality control technical replicates (TR) and digestion replicates (DR). Plasma aliquot was shunted to Top14 Abundant Protein Depletion Resin (A36372) based depletion. Depleted plasma samples were processed on a i7 automated liquid handling system (Beckman Coulter) in a 96-well plate for protein denaturation, cysteine reduction and alkylation, and trypsin digestion. Healthy control pooled samples were used as DRs and embedded between samples during digestion. Depleted plasma tryptic peptides were separated by EVOSEP One LC System (Evosep) over a 45-minute gradient injected into an Orbitrap Exploris 480 MS (Thermo Fisher) using DIA-MS settings as described by McArdle and Binek et. al. During MS acquisition, the 4 DRs are run at the beginning of each batch. In addition, pooled, bulk digested plasma samples from Parkinsons Disease patients are included as technical replicates (TRs) at the beginning and middle of every MS batch, with the goal of assessing LC-MS performance.
HostingRepository	MassIVE
AnnounceDate	2025-06-23
AnnouncementXML	Submission_2025-06-23_12:30:21.434.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 13:27:51	ID requested
⏵ 1	2025-06-23 12:30:22	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: Quality Control, DIA, Digestion Replicates, Technical Replicates, Depleted Plasma

submitter keyword: Quality Control, DIA, Digestion Replicates, Technical Replicates, Depleted 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
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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/MSV000095742/