Proteomics

Dataset Information

0

Systematic Evaluation and Optimization of Protein Extraction Parameters in Diagnostic FFPE Specimens


ABSTRACT: Objectives: Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for di-agnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction pro-tocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of func-tionally relevant proteins. Methods: Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was meas-ured by protein concentration and western blot analysis of cellular compart-ment markers as well as liquid chromatography-coupled mass spectrometry (LC-MS). Results: Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions: Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urinary Bladder

SUBMITTER: Franz Friedrich Dressler  

LAB HEAD: Franz Dressler

PROVIDER: PXD029133 | Pride | 2022-05-19

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
20201106_2020-12_1.1.wiff Wiff
20201106_2020-12_1.1.wiff.scan Wiff
20201106_2020-12_2.1.wiff Wiff
20201106_2020-12_2.1.wiff.scan Wiff
20201106_2020-12_3.1.wiff Wiff
Items per page:
1 - 5 of 21
altmetric image

Publications

Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens.

Dressler Franz F FF   Schoenfeld Jana J   Revyakina Olga O   Vogele Daniel D   Kiefer Selina S   Kirfel Jutta J   Gemoll Timo T   Perner Sven S  

Clinical proteomics 20220502 1


<h4>Objectives</h4>Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservati  ...[more]

Similar Datasets

2019-03-18 | GSE128202 | GEO
2020-03-05 | PXD016563 | Pride
2019-11-15 | PXD015981 | Pride
2018-06-06 | PXD008656 | Pride
2021-09-10 | PXD023891 | Pride
2018-01-08 | PXD006255 | Pride
2011-09-15 | GSE31735 | GEO
2021-05-05 | PXD024800 | Pride
2021-10-26 | GSE162443 | GEO
2024-05-21 | PXD036910 | Pride