Dataset Information

The effect of polyethylene glycol 20,000 on protein extraction efficiency of formalin-fixed, paraffin-embedded tissues

ABSTRACT: The optimal conditions and procedures for efficient and reproducible protein extraction of FFPE tissues have not yet been standardised and new sensitive techniques are continually being developed and improved upon. To our knowledge, there is no general agreement as to the choice of detergent or buffer system (and/or addition of PEG 20,000) required for efficient and reproducible protein extraction from human FFPE tissues. Moreover, the effect of PEG 20,000 on protein extraction efficiency has not been evaluated using human FFPE colorectal cancer tissues. This study therefore aims to assess the impact of PEG 20,000 on the protein extraction efficiency, reproducibility, and protein selection bias of the protein extraction buffer used for FFPE colonic resection tissue in label-free LC-MS/MS analysis. The sample pellets were also tested for residual protein, not extracted in the initial extraction. The results show that the absence of PEG 20,000 increases the number of peptides and proteins identified by unfractionated LC-MS/MS analysis, and the method is more reproducible. However, no significant differences were observed with regard to protein selection bias. We propose that studies generating high protein yields would benefit from the absence of PEG 20,000 in the protein extraction buffer.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Colon

DISEASE(S): Colon Cancer

SUBMITTER: Catherine Rossouw

LAB HEAD: Alan Christoffels

PROVIDER: PXD014419 | Pride | 2022-02-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1068_Pellet_PEG_HILIC_1.mgf	Mgf
	1068_Pellet_PEG_HILIC_1.msgf.mzid.gz	Mzid
	1068_Pellet_PEG_HILIC_1.msgf.pride.mztab.gz	Mztab
	1068_Pellet_PEG_HILIC_1.pride.mgf.gz	Mgf
	1068_Pellet_PEG_HILIC_1.raw	Raw

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Publications

Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa.

Rossouw Sophia S Bendou Hocine H Bell Liam L Rigby Jonathan J Christoffels Alan A

African journal of laboratory medicine 20211217 1

<h4>Background</h4>Optimal protocols for efficient and reproducible protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues are not yet standardised and new techniques are continually developed and improved. The effect of polyethylene glycol (PEG) 20 000 on protein extraction efficiency has not been evaluated using human FFPE colorectal cancer tissues and there is no consensus on the protein extraction solution required for efficient, reproducible extraction.<h4>Objective</h4>The ...[more]

PMID: 34966662

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