STOREDB:STUDY1009 FFPE qualitative proteomics [DOI:10.20348/STOREDB/1009]

Study meta-data


STUDYIDSTOREDB:STUDY1009
CREATEDON2015-12-10 12:36:28
MODIFIEDON2016-04-01 12:34:15
UPLOADEROmid Azimzadeh
DOIDOI:10.20348/STOREDB/1009

Study details


STUDY NAME
FFPE qualitative proteomics
STUDY STATUS
Published: Open access to everyone
DATA SHARING POLICY
CC-Attribution
COUNTRY
Germany
PRINCIPAL INVESTIGATOR
Dr. Omid Azimzadeh
BIOLOGICAL SAMPLE AVAILABLE
No
STUDY DESCRIPTION
Formalin-fixed paraffin embedded (FFPE) tissue has recently gained interest as an alternative to fresh/frozen tissue for retrospective protein biomarker discovery. However, during the fixation process proteins undergo degradation and cross-linking, making conventional protein analysis technologies problematic. In this study we have compared several extraction and separation methods for the analysis of proteins in FFPE tissues. Incubation of tissue sections at high temperature with a novel extraction buffer (20 mM Tris-HCl, pH 8.8, 2% SDS, 1% beta-octylglucoside, 200 mM DTT, 200 mM glycine and a mixture of protease inhibitors), resulted in improved protein recovery. Protein separation by 1-DE followed by LC-ESI MS/MS analysis was the most effective approach to identify proteins, based on the number of peptides reliably identified. Interestingly, a number of peptides were identified in regions of the 1DE not corresponding to their native molecular weights. This is an indication of the formation of protein-protein complexes by cross-linking, and to protein fragmentation due to prolonged sample storage.This study will facilitate the development of future proteomic analysis of FFPE tissue and provide a tool for the validation in archival samples of biomarkers of exposure, prognosis and disease.
http://pubs.acs.org/doi/pdfplus/10.1021/pr1004168
STOREV2_PROJECTID
http://131.111.32.76/store/project_details.php?projectid=2 (This project has originally been uploaded into the STORE v2 system and is still available here)

STOREDB:DATASET1017 MS raw data [DOI:10.20348/STOREDB/1009/1017]


Created on:2015-12-10 12:38:47 Modified On:2015-12-10 12:38:47
DATASET NAME
MS raw data
DOIDOI:10.20348/STOREDB/1009/1017
DATASET DESCRIPTION
MS MS spectra Run-5_uniref_mus
STOREV2_DATASETID
http://131.111.32.76/store/dataset_details.php?datasetid=15 (This dataset has originally been uploaded into the STORE v2 system and is still available here)

STOREDB:DATASET1016 Protein identifications [DOI:10.20348/STOREDB/1009/1016]


Created on:2015-12-10 12:37:55 Modified On:2015-12-10 12:37:55
DATASET NAME
Protein identifications
DOIDOI:10.20348/STOREDB/1009/1016
DATASET DESCRIPTION
LC MSMS FFPE protein identifications
STOREV2_DATASETID
http://131.111.32.76/store/dataset_details.php?datasetid=14 (This dataset has originally been uploaded into the STORE v2 system and is still available here)

STOREDB:DATASET1015 FFPE gel separation figures [DOI:10.20348/STOREDB/1009/1015]


Created on:2015-12-10 12:37:11 Modified On:2015-12-10 12:37:11
DATASET NAME
FFPE gel separation figures
DOIDOI:10.20348/STOREDB/1009/1015
DATASET DESCRIPTION
FFPE protein extraction using different detergent containing buffers
STOREV2_DATASETID
http://131.111.32.76/store/dataset_details.php?datasetid=13 (This dataset has originally been uploaded into the STORE v2 system and is still available here)