PXD014419-1

PXD014419 is an original dataset announced via ProteomeXchange.

Title	The effect of polyethylene glycol 20,000 on protein extraction efficiency of formalin-fixed, paraffin-embedded tissues
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-02-15
AnnouncementXML	Submission_2022-02-15_09:01:19.663.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD014419
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Catherine Rossouw
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Methylthio; Deamidated; Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-28 01:08:55	ID requested
⏵ 1	2022-02-15 09:01:20	announced

Rossouw S, Bendou H, Bell L, Rigby J, Christoffels A, Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa. Afr J Lab Med, 10(1):1122(2021) [pubmed]

submitter keyword: Mass spectrometry, FFPE proteomics, Archival tissue, protein extraction, PEG-20,000, SP3-on-bead-digestion

Alan Christoffels
contact affiliation	South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, South Africa
contact email	alan@sanbi.ac.za
lab head
Catherine Rossouw
contact affiliation	University of the Western Cape
contact email	sc.rossouw@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014419
     1. Label: PRIDE project
     2. Name: The effect of polyethylene glycol 20,000 on protein extraction efficiency of formalin-fixed, paraffin-embedded tissues