PXD065609-1

PXD065609 is an original dataset announced via ProteomeXchange.

Title	Plasma Protein Partition by Acetonitrile and Polyethylene Glycol Boosts Proteome Coverage
Description	Limited proteome coverage is a common challenge in plasma or serum proteomic analysis. We find that sequential precipitation of plasma by increasing concentrations of acetonitrile yields distinct subsets of proteins. Deep analysis of the original whole plasma (Plasma), the pellets of plasma precipitated sequentially by 40% acetonitrile (40AcN_pellet) and further by 50% acetonitrile (50AcN_pellet), and the final supernatant (50AcN_Sup), have profiled 2040, 2078, 1153 and 1414 proteins respectively, yielding 3386 proteins in total. In addition, the plasma was also isolated by 10% and 20% PEG6000 precipitation followed by albumin depletion (10PEG/Alb-/-, 20PEG/Alb-/-) as we have previously reported (Anal Chem 2025, PMID: 40468192). Combination of these six samples (6mix), including: 1) the original plasma, 2) 20AcN_pellet (precipitate of plasma by 20% acetonitrile), 3) 40AcN_pellet, 4) 50AcN_Sup, 5) 10PEG/Alb-/-, and 6) 20PEG/Alb-/- has led to identification of 5441 proteins (5356 genes), increasing the proteome coverage remarkably. Plasma sample used for these analyses were pooled from 100 clinical samples (80 patients with different types of diseases + 20 visitors for health screening). Samples for the five in-depth proteomic datasets are: Plasma (the original whole plasma), 40AcN_pellet (the pellet of plasma precipitated by 40% acetonitrile), 50AcN_pellet (the pellet of the plasma was first precipitated by 40% acetonitrile and then by 50% acetonitrile), 50AcN_Sup (the final supernatant of plasma after precipitation by 50% acetonitrile), and 6mix (the equal mixture of the plasma and the five isolates as mentioned).
HostingRepository	iProX
AnnounceDate	2025-06-30
AnnouncementXML	Submission_2025-06-30_00:41:30.701.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bing Bai
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-30 00:41:04	ID requested
⏵ 1	2025-06-30 00:41:31	announced

Dataset with its publication pending

submitter keyword: Plasma, acetonitrile, polyethylene glycol, albumin depletion, proteomics

Bing Bai
contact affiliation	Nanjing University
contact email	bing.bai@nju.edu.cn
lab head
Bing Bai
contact affiliation	Nanjing University
contact email	bing.bai@nju.edu.cn
dataset submitter

iProX dataset URI