PXD002526 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
Keyword List
curator keyword: Technical |
submitter keyword: protein extraction,proteomics, ffpe, quantification |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002526
- Label: PRIDE project
- Name: Temperature, Oil and Pressure (TOP) extraction: optimal sample preparation for proteomic analysis of formalin fixed paraffin embedded tissue