Dataset Information

HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies

ABSTRACT: Hepes-glutamic acid buffer mediated Organic solvent Protection Effect (HOPE)-fixation has been introduced as an alternative to formalin fixation of clinical samples. Beyond preservation of morphological structures for histology, HOPE-fixation was demonstrated to be compatible with recent methods for RNA and DNA sequencing. However, suitability of HOPE-fixed materials for the inspection of proteomes by mass spectrometry so far remained undefined. This is of particular interest, since proteins constitute a prime resource for drug research and can give valuable insights into the activity status of signaling pathways. In this study, we extracted proteins from human lung tissue and tested HOPE-treated and snap frozen tissues comparatively by proteome and phosphoproteome analyses. High confident data from accurate mass spectrometry allowed the identification of 2603 proteins and 3036 phosphorylation sites. HOPE-fixation did not hinder the representative extraction of proteins and investigating their biochemical properties, covered subcellular localizations and cellular processes revealed no bias caused by the type of fixation. In conclusion, proteome as well as phosphoproteome data of HOPE lung samples were qualitatively equivalent to results obtained from snap frozen tissues. Thus, HOPE-treated tissues match clinical demands both in histology and retrospective proteome analyses of patient samples by proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Olga Shevchuk

LAB HEAD: Lothar Jänsch

PROVIDER: PXD000836 | Pride | 2014-05-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	PhosphoproteomeHOPE.msf	Msf
	PhosphoproteomeHOPE.prot.xml	Xml
	PhosphoproteomeHOPE1.raw	Raw
	PhosphoproteomeHOPE2.raw	Raw
	PhosphoproteomeHOPE3.raw	Raw

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HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies.

Shevchuk Olga O Abidi Nada N Klawonn Frank F Wissing Josef J Nimtz Manfred M Kugler Christian C Steinert Michael M Goldmann Torsten T Jänsch Lothar L

Journal of proteome research 20140428 11

Hepes-glutamic acid buffer-mediated organic solvent protection effect (HOPE)-fixation has been introduced as an alternative to formalin fixation of clinical samples. Beyond preservation of morphological structures for histology, HOPE-fixation was demonstrated to be compatible with recent methods for RNA and DNA sequencing. However, the suitability of HOPE-fixed materials for the inspection of proteomes by mass spectrometry so far remained undefined. This is of particular interest, since proteins ...[more]

PMID: 24702127

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