PXD029133

PXD029133 is an original dataset announced via ProteomeXchange.

Title	Systematic Evaluation and Optimization of Protein Extraction Parameters in Diagnostic FFPE Specimens
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-05-19
AnnouncementXML	Submission_2022-05-19_06:45:51.761.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Franz Friedrich Dressler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; acetylated residue; monohydroxylated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-14 07:59:54	ID requested
⏵ 1	2022-05-19 06:45:52	announced

Dressler FF, Schoenfeld J, Revyakina O, Vogele D, Kiefer S, Kirfel J, Gemoll T, Perner S, Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens. Clin Proteomics, 19(1):10(2022) [pubmed]

submitter keyword: Protein extraction

formalin-fixed paraffin-embedded tissue

clinical prote-omics

antigen retrieval

crosslinking reversal

protein analysis

biomarker

Franz Dressler
contact affiliation	Institute of Pathology, University Medical Center Schleswig-Holstein, Lubeck Site
contact email	franzfriedrich.dressler@uksh.de
lab head
Franz Friedrich Dressler
contact affiliation	University Medical Center Schleswig-Holstein, Luebeck
contact email	franz.dressler@web.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029133
     1. Label: PRIDE project
     2. Name: Systematic Evaluation and Optimization of Protein Extraction Parameters in Diagnostic FFPE Specimens