PXD002169

PXD002169 is an original dataset announced via ProteomeXchange.

Title	Fixated rat liver tissue
Description	Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced cross-links, fixated tissue proteins are difficult to extract hampering the performance of mass spectrometry (MS)-proteomic analysis on formaldehyde-fixated tissue. Recent years saw the use of different combinations of high-temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixated paraffin-embedded tissue proteomes. However, in order to achieve protein extraction yields similar to fresh-frozen tissue high-temperature heating is necessary. Such harsh extraction conditions may affect, labile post-translational modifications such as phosphorylations resulting in the loss of important protein information. The objective of the present work is to assess cleavable fixative reagents that allow tissue preservation as well as efficient protein extraction from fixated tissue for MS-proteomics under mild conditions. To this regard, we investigated disuccinimidyl tartrate (DST) and dithiobis[succinimidylpropionate] (DSP) as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups leading to amide bond formation. Linkers can be cleaved with sodium metaperiodate (cis-diols) or reducing agents (disulfide bonds), respectively. Our results show that reversible protein crosslinking allows tissue fixation with morphology preservation comparable to formalin. In addition, cleavage of DSP improves protein recovery from fixated tissue by a factor of 18 and increases the number of identified proteins by approximately 20% under mild extraction conditions avoiding the need for sample boiling, which could affect labile post-translational modifications. A major advantage of DSP over formaldehyde is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by periodic cleavage, while effective, resulted in side reactions that prevented effective protein extraction and subsequent protein identification. Protein crosslinkers, which can be cleaved under mild conditions, are thus viable alternatives to formaldehyde as tissue fixatives facilitating protein analysis from paraffin embedded, fixated tissue.
HostingRepository	PRIDE
AnnounceDate	2018-01-29
AnnouncementXML	Submission_2018-01-29_09:45:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sara Ongay
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-05-12 03:12:33	ID requested
⏵ 1	2018-01-29 09:45:57	announced

Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R, Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis. Chembiochem, 19(7):736-743(2018) [pubmed]

curator keyword: Technical

submitter keyword: Rat liver, tissue fixation, cleavable crosslinkers, reversible crosslinking

Rainer Bischoff
contact affiliation	University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands, Tel. +31-50-363-3338 (secr. 3336), Fax +31-50-363-7582, r.p.h.bischoff@rug.nl.
contact email	r.p.h.bischoff@rug.nl
lab head
Sara Ongay
contact affiliation	RUG
contact email	s.ongay.camacho@rug.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD002169

PRIDE project URI

• PRIDE
  1. PXD002169
     1. Label: PRIDE project
     2. Name: Fixated rat liver tissue