STUDYID | STOREDB:STUDY1009 |
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CREATEDON | 2015-12-10 12:36:28 |
MODIFIEDON | 2020-09-24 16:37:31 |
UPLOADER | Omid Azimzadeh |
DOI | DOI:10.20348/STOREDB/1009 |
STUDY NAME | ||
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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 |
DATASET NAME | ||
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MS raw data | ||
DOI | DOI:10.20348/STOREDB/1009/1017 | |
DATASET DESCRIPTION | ||
MS MS spectra Run-5_uniref_mus |
Type: text/plain
File size: 13 kilobytes
Uploaded on: 2020-09-24 16:36:41
DATASET NAME | ||
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Protein identifications | ||
DOI | DOI:10.20348/STOREDB/1009/1016 | |
DATASET DESCRIPTION | ||
LC MSMS FFPE protein identifications |
Type: application/vnd.ms-excel
File size: 139 kilobytes
Uploaded on: 2020-09-24 16:36:08
DATASET NAME | ||
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FFPE gel separation figures | ||
DOI | DOI:10.20348/STOREDB/1009/1015 | |
DATASET DESCRIPTION | ||
FFPE protein extraction using different detergent containing buffers |
Type: image/tiff
File size: 1 megabytes
Uploaded on: 2020-09-24 16:35:27