PXD000836 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2014-05-22 |
AnnouncementXML | Submission_2014-05-22_03:37:04.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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: lung tissues, HOPE-fixation technique, proteome, post-translational modifications, phosphorylation, biobank, LC-MS/MS |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000836
- Label: PRIDE project
- Name: HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies