PXD002526

PXD002526 is an original dataset announced via ProteomeXchange.

Title	Temperature, Oil and Pressure (TOP) extraction: optimal sample preparation for proteomic analysis of formalin fixed paraffin embedded tissue
Description	Formalin-fixed paraffin embedded (FFPE) is the clinical gold standard of tissue preservation globally. We present a novel method for optimal extraction of proteins from FFPE tissue samples. The method combines non-toxic, proteomic inert mineral oil for deparaffinization, followed by extraction using elevated temperature and pressure (121˚C; 15 psi). Our novel TOP (Temperature, Oil, and Pressure) proteome extraction is four times faster, less laborious and increases the protein yield. Furthermore, the TOP method is environmentally friendly, as opposed to traditional methods. Comparison of extracted protein by mass spectrometry based proteomics revealed that TOP is not sensitive to formalin over-fixation, unlike the traditional approach, a fact that makes it suitable in the clinical setting. We expect that the TOP proteome extraction platform will help to alleviate some of the difficulties proteomics is facing in the clinical setting.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:29:02.284.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yishai Levin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-13 02:34:29	ID requested
1	2024-02-11 23:07:21	announced
⏵ 2	2024-10-22 06:29:02	announced	2024-10-22: Updated project metadata.

10.1074/MCP.RA120.002152;

curator keyword: Technical

submitter keyword: protein extraction,proteomics, ffpe, quantification

Yishai Levin
contact affiliation	Weizmann Institute of Science
contact email	yishai.levin@gmail.com
lab head
Yishai Levin
contact affiliation	Weizmann Institute of Science, Israel
contact email	yishai.levin@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002526
     1. Label: PRIDE project
     2. Name: Temperature, Oil and Pressure (TOP) extraction: optimal sample preparation for proteomic analysis of formalin fixed paraffin embedded tissue