PXD012436-2

PXD012436 is an original dataset announced via ProteomeXchange.

Title	An ultrafast, reliable and economical approach for quantitative salivary proteomic profiling and oral cancer biomarker discovery
Description	Clinical biomarkers identified by shotgun proteomics require proteins in body fluids or tissues to be enzymatically digested before being separated and sequenced by Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS). How well peptide signals can be resolved and detected is largely dependent on the quality of sample preparation. Conventional approaches such as in-gel, in-solution, and filter-based digestion, despite their extensive implementation by the community, become less appealing due to their unsatisfying protein/peptide recovery rate, lengthy sample processing, and/or less cost-effectiveness. Suspension Trapping has recently been demonstrated as an ultrafast approach for proteomics analysis. Here, for the first time, we extend its application to human salivary proteome analyses. In particular, we present a simple self-assembled glass fiber filter device, which can be packed with minimal difficulty, is extremely cost-effective and maintains the same performances as commercial filters. As a proof-of-principle, we analyzed the whole saliva from 8 healthy individuals as well as a cohort of 10 subjects of oral squamous cell carcinoma (OSCC) patients and non-OSCC subjects. Label-free quantification revealed surprisingly low inter-individual variability, and identified several known markers. Our study provides the first evidence of an easy-to-use and nearly cost-free device for clinical proteomics as well as for general proteome sample preparation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:52:46.728.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yanbao Yu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-20 23:50:37	ID requested
1	2019-03-11 23:00:02	announced
⏵ 2	2024-10-22 04:52:50	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.9b00037;

Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y, Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery. J Proteome Res, 18(4):1907-1915(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: STrap, Saliva,Suspension Trapping, HeLa, Clinical Proteomics, oral squamous cell carcinoma, FASP, Biomarker, OSCC

Yanbao Yu
contact affiliation	J. Craig Venter Institute, Rockville, MD 20850
contact email	yayu@jcvi.org
lab head
Yanbao Yu
contact affiliation	University of Delaware
contact email	yayu@jcvi.org
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/2019/03/PXD012436

PRIDE project URI

• PRIDE
  1. PXD012436
     1. Label: PRIDE project
     2. Name: An ultrafast, reliable and economical approach for quantitative salivary proteomic profiling and oral cancer biomarker discovery