PXD023891

PXD023891 is an original dataset announced via ProteomeXchange.

Title	Protein extraction method improvement for FFPE kidney tissue samples
Description	The vast majority of tissue biopsies from patients in hospital environments are included in paraffin (FFPE- formalin-fixed and paraffin-embedded) for long-term storage. This fixation process produces a modification in the proteins called "crosslinks", which improves protein stability, necessary for their conservation. Currently, these samples are mainly used in clinical practice for performing immunohistochemical techniques, since these modifications do not suppose a drawback for this technique; however, crosslinks makes the protein extraction process a challenging one. Accordingly, these modifications make the development of a good protein extraction protocol necessary. Due to the specific characteristics of each tissue, the same extraction buffers or deparaffinization protocols are not equally effective in all cases. Therefore, it is necessary to obtain a specific protocol for each tissue. This work aims to establish a deparaffinization and protein extraction protocol from paraffin-embedded kidney samples, which finally allows us to obtain high quantity and quality protein, suitable for the application of proteomic techniques. To achieve this; we have designed different protocols using a range of buffers with diverse compositions and characteristics. Our results showed that xylene can eliminate the formalin fixation from the kidney tissue. Moreover, strong detergents (SDS-sodium dodecil sulfate- or analogues) and reducing agents (e.g. DTT- Dithiothreitol-) in the extraction buffer appear to be more important to obtain a good protein extraction yields and a good number of proteins identifications by LC-MSMS.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_14:07:48.153.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susana Bravo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-29 08:20:16	ID requested
⏵ 1	2022-02-16 14:07:49	announced

Garc, í, a-Vence M, Chantada-Vazquez MDP, Sosa-Fajardo A, Agra R, Barcia de la Iglesia A, Otero-Glez A, Garc, í, a-Gonz, á, lez M, Cameselle-Teijeiro JM, Nu, ñ, ez C, Bravo JJ, Bravo SB, Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques. Front Med (Lausanne), 8():657313(2021) [pubmed]

submitter keyword: Deparaffinization

proteins extraction

Formalin-fixed paraffin-embedded (FFPE) samples

proteomic approaches

LC-MALDI-MS

LC-MS/MS

methylene bridges

Susana Belen Bravo Lopez
contact affiliation	proteomic facillity- Instituto de Investigaciones Sanitarias de Santiago de Compostela
contact email	sbbravo@gmail.com
lab head
Susana Bravo
contact affiliation	FIDIS
contact email	sbbravo@gmail.com
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/2021/09/PXD023891

PRIDE project URI

• PRIDE
  1. PXD023891
     1. Label: PRIDE project
     2. Name: Protein extraction method improvement for FFPE kidney tissue samples