PXD002029

PXD002029 is an original dataset announced via ProteomeXchange.

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	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:24:27.741.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tue Bjerg Bennike
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

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.

10.1016/j.dib.2016.01.061;

Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A, Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies. Data Brief, 6():942-7(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, snap-frozen, proteomics, mucosa, LC-MS, FFPE, RNAlater, colon, stability

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 Bjerg Bennike
contact affiliation	Aalborg University
contact email	tbe@hst.aau.dk
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/2015/11/PXD002029

PRIDE project URI

• PRIDE
  1. PXD002029
     1. Label: PRIDE project
     2. Name: Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies