PXD050216

PXD050216 is an original dataset announced via ProteomeXchange.

Title	Characterization of Protein Precipitation Methods of Clinical Samples for Simple and Low-Cost Methods to Enhance the Depth and Breadth of Plasma Proteomics
Description	Plasma is an abundant source of proteins and potential biomarkers to aid in the detection, diagnosis, and prognosis of human diseases. However, these proteins are often present at low levels in the blood and difficult to consistently identify and measure. Quantifying more than a few hundred proteins in neat plasma is difficult due to the large dynamic range, and as much as ~99% of its mass is derived from only ~20 proteins. Abundant protein precipitation with perchloric acid (PerCA) is a high-throughput approach to increase protein identifications and depth of plasma proteomic studies. The goal of this work was to characterize and compare various protein precipitation methods related to plasma proteomic depth and breadth. Three acid-based and four solvent-based precipitation methods were evaluated by mass spectrometry. All methods tested provided excellent plasma proteomic coverage (>600 identified protein groups) and detected protein in the low pg/ml range. Functional enrichment analysis revealed subtle differences within and larger changes between the precipitant groups; acid-based methods enriched for plasma membrane proteins, while solvent-based approaches enriched for lipoprotein particle proteins. Methanol-based precipitation outperformed the other methods based on identifications and reproducibility. The performance of these methods was verified using eight lung cancer patient samples, where >700 protein groups were measured and proteins with an estimated plasma concentration of around 10 pg/ml were detected. In conclusion, a variety of protein precipitation agents are amenable to extending the depth and breadth of plasma proteomes, however, the composition of proteins between agents does vary. These data can guide investigators to implement inexpensive, high-throughput methods for their plasma proteomic workflows.
HostingRepository	PRIDE
AnnounceDate	2025-05-29
AnnouncementXML	Submission_2025-05-29_05:27:13.049.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shawn Rice
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF fleX

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-28 08:24:55	ID requested
⏵ 1	2025-05-29 05:27:13	announced

Dataset with its publication pending

submitter keyword: Plasma, Depletion, Perchloric acid, methanol, Proteomics

Chandra P. Belani
contact affiliation	Penn State College of Medicine, Department of Medicine, Penn State Cancer Institute.
contact email	cbelani@pennstatehealth.psu.edu
lab head
Shawn Rice
contact affiliation	Penn State College of Medicine
contact email	srice@pennstatehealth.psu.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/2025/05/PXD050216

PRIDE project URI

• PRIDE
  1. PXD050216
     1. Label: PRIDE project
     2. Name: Characterization of Protein Precipitation Methods of Clinical Samples for Simple and Low-Cost Methods to Enhance the Depth and Breadth of Plasma Proteomics