PXD000836

PXD000836 is an original dataset announced via ProteomeXchange.

Title	HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies
Description	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.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:52:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Olga Shevchuk
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; phosphorylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-03-17 03:41:27	ID requested
1	2014-05-22 03:37:05	announced
⏵ 2	2014-07-25 01:52:38	announced	Updated project metadata.

Shevchuk O, Abidi N, Klawonn F, Wissing J, Nimtz M, Kugler C, Steinert M, Goldmann T, J, ä, nsch L, HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies. J Proteome Res, 13(11):5230-9(2014) [pubmed]

submitter keyword: lung tissues, HOPE-fixation technique, proteome, post-translational modifications, phosphorylation, biobank, LC-MS/MS

Lothar Jänsch
contact affiliation	Helmholtz Center for Infection Research
contact email	Lothar.Jaensch@helmholtz-hzi.de
lab head
Olga Shevchuk
contact affiliation	CPRO
contact email	Olga.Shevchuk@helmholtz-hzi.de
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/2014/05/PXD000836

PRIDE project URI

• PRIDE
  1. PXD000836
     1. Label: PRIDE project
     2. Name: HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies