Proteomics

Dataset Information

0

Biopsy proteome scoring to determine mucosal remodeling in celiac disease


ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Anette Johansen  

LAB HEAD: Jorunn Stamnæs

PROVIDER: PXD045913 | Pride | 2024-03-15

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
1a-4b.zip Other
A1Anette.raw Raw
A1Anette_220608022510.raw Raw
A2Anette.raw Raw
A2Anette_220608045028.raw Raw
Items per page:
1 - 5 of 165

Similar Datasets

2016-03-09 | E-GEOD-72220 | biostudies-arrayexpress
2019-04-25 | PXD011681 | Pride
2005-06-22 | E-MEXP-367 | biostudies-arrayexpress
2023-04-06 | PXD035854 | Pride
2018-11-21 | PXD008992 | Pride
2023-04-06 | PXD035853 | Pride
2013-08-23 | E-GEOD-50084 | biostudies-arrayexpress
2006-06-16 | E-TABM-104 | biostudies-arrayexpress
2024-04-05 | PXD046365 | Pride
2023-05-23 | PXD026709 | Pride