PXD016261

PXD016261 is an original dataset announced via ProteomeXchange.

Title	Evaluation of tumor interstitial fluid-extraction methods for proteome analysis: comparison of biopsy elution versus centrifugation
Description	The analysis of Tumor Interstitial Fluid (TIF) composition is a valuable procedure to identify anti-metastatic targets, and different laboratories have set up techniques for TIF isolation and proteomic analyses. However, those methods had never been compared in samples from the same tumor and patient. In this work, we compared the two most used methods, elution and centrifugation, in pieces of the same biopsy samples of cutaneous squamous cell carcinoma (cSCC). First, we established that high G-force (10000g) was required to obtain TIF from cSCC by centrifugation. Secondly, we compared the centrifugation method with the elution method in pieces of three different cSCC tumors. We found that the mean protein intensities based in the number of peptide spectrum matches was significantly higher in the centrifuged samples than in the eluted samples. Regarding the robustness of the methods, we observed higher overlapping between both methods (77-80%) than among samples (50%). These results suggest that exists an elevated consistence of TIF composition independently of the method used. However, we observed a three-fold increase of extracellular proteins in non-overlapped proteome obtained by centrifugation. We therefore conclude that centrifugation is the method of choice to study the proteome of TIF from cutaneous biopsies.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:03:20.987.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joan Josep Bech-Serra
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-13 03:54:23	ID requested
1	2020-05-06 06:08:28	announced
⏵ 2	2024-10-22 05:03:24	announced	2024-10-22: Updated project metadata.

Matas-Nadal C, Bech-Serra JJ, Guasch-Vall, é, s M, Fern, á, ndez-Armenteros JM, Barcel, ó C, Casanova JM, de la Torre G, ó, mez C, Aguayo Ortiz R, Gar, í E, Evaluation of Tumor Interstitial Fluid-Extraction Methods for Proteome Analysis: Comparison of Biopsy Elution versus Centrifugation. J Proteome Res, 19(7):2598-2605(2020) [pubmed]

10.1021/acs.jproteome.9b00770;

submitter keyword: cutaneous squamous cell carcinoma, skin cancer,Tumor interstitial fluid, spin, proteome, centrifugation, elution

Eloi Gari
contact affiliation	Cell cycle lab. Institut de Recerca Biomèdica de Lleida (IRB Lleida).
contact email	eloi.gari@cmb.udl.cat
lab head
Joan Josep Bech-Serra
contact affiliation	Proteomics Unit - Josep Carreras Leukaemia Research Institute
contact email	jbech@carrerasresearch.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/2020/05/PXD016261

PRIDE project URI

• PRIDE
  1. PXD016261
     1. Label: PRIDE project
     2. Name: Evaluation of tumor interstitial fluid-extraction methods for proteome analysis: comparison of biopsy elution versus centrifugation