PXD002029 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies |
Description | Clinical proteomics research is in part limited by the availability of clinical samples. However, large biobanks exist worldwide containing formalin-fixed and paraffin embedded samples and samples stored in RNAlater. The extraction of proteins for proteome analysis from samples prepared by either method has been demonstrated. However, the impact of the preservation method on the result of a quantitative proteome analysis remains largely uninvestigated. We, therefore, conducted a proteome analysis of human colon mucosal biopsies where the material had been preserved accordingly. Twenty-four colon mucosal biopsies were extracted from the sigmoideum by endoscopy from two participants. The biopsies were either directly-frozen, stabilized in RNAlater, or stabilized by formaldehyde fixation immediately or incubated for 30 min to simulate a clinical situation, followed by paraffin embedding. The impact of the preservation method on the result of a proteome analysis was characterized by high throughput gel free quantitative proteomics. |
HostingRepository | PRIDE |
AnnounceDate | 2015-11-23 |
AnnouncementXML | Submission_2015-11-23_14:12:19.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Tue Bennike |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-04-08 01:49:13 | ID requested | |
⏵ 1 | 2015-11-23 14:12:20 | announced | |
2 | 2016-03-09 02:19:01 | announced | Updated publication reference for PubMed record(s): 26937473. |
3 | 2024-10-22 04:24:35 | announced | 2024-10-22: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Biomedical |
submitter keyword: Human, colon, mucosa, RNAlater, FFPE, snap-frozen, stability, LC-MS, proteomics |
Contact List
Allan Stensballe |
contact affiliation | Laboratory for Medical Mass Spectrometry Department of Health Science and Technology Aalborg University Denmark |
contact email | as@hst.aau.dk |
lab head | |
Tue Bennike |
contact affiliation | Aalborg University |
contact email | tbe@hst.aau.dk |
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/2015/11/PXD002029 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002029
- Label: PRIDE project
- Name: Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies