PXD054650

PXD054650 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples
Description	We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from very low starting input in a scalable format that is useful to decipher the alterations in tumor and the stromal microenvironment. Correlating such results with clinical features or disease progression will likely enable identification of novel targets for disease classification and interventions.
HostingRepository	jPOST
AnnounceDate	2025-08-07
AnnouncementXML	Submission_2025-08-06_08:00:31.187.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aswini Panigrahi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue
Instrument	timsTOF HT

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-06 14:12:37	ID requested
⏵ 1	2025-08-06 08:00:31	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: HNSCC, FFPE, LMD, diaPASEF

submitter keyword: HNSCC, FFPE, LMD, diaPASEF

Contact List

Radoslav Goldman
lab head
Aswini Panigrahi
contact affiliation	Georgetown University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST 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://ftp.jpostdb.org/JPST003262/