PXD045913-1

PXD045913 is an original dataset announced via ProteomeXchange.

Title	Biopsy proteome scoring to determine mucosal remodeling in celiac disease
Description	For celiac disease (CeD) the diagnosis and response to treatment is determined by histological evaluation of gut biopsies which depend on proper biopsy orientation and has poor inter-observer reproducibility. Biopsy proteome measurement that reports on the tissue state can be obtained by mass spectrometry (MS) analysis of formalin-fixed paraffin embedded (FFPE) tissue. Here we aimed to transform biopsy proteome data into numerical scores that would give observer-independent measures of mucosal remodeling in CeD. A pipeline was established that employs glass-mounted FFPE sections for MS-based proteome analysis. Proteome data was converted to a numerical score using two different approaches, by calculating a rank-based enrichment score and by training a machine-learning algorithm to calculate a disease-state prediction value. The scoring approaches were compared to each other and to histology using a validation cohort of 18 CeD patients comparing biopsies collected before and after treatment with gluten-free diet (GFD). Biopsies from non-CeD individuals (n = 18) served as controls.
HostingRepository	PRIDE
AnnounceDate	2024-03-15
AnnouncementXML	Submission_2024-03-15_09:17:08.521.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anette Johansen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-05 07:36:57	ID requested
⏵ 1	2024-03-15 09:17:08	announced
2	2024-10-22 06:33:36	announced	2024-10-22: Updated project metadata.

10.1053/J.GASTRO.2024.03.006;

submitter keyword: LC-MSMS, machine learning, molecular histology, clinical proteomics,celiac disease

Jorunn Stamnæs
contact affiliation	Department of Immunology, University of Oslo, Norway
contact email	jorunn.stamnas@medisin.uio.no
lab head
Anette Johansen
contact affiliation	University of Oslo
contact email	anette.johansen@medisin.uio.no
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/2024/03/PXD045913

PRIDE project URI

• PRIDE
  1. PXD045913
     1. Label: PRIDE project
     2. Name: Biopsy proteome scoring to determine mucosal remodeling in celiac disease