Effective protein extraction combined with data independent acquisition analysis reveals a comprehensive and quantifiable insight into the proteomes of articular cartilage and subchondral bone
Bundgaard, Louise LU ; Åhrman, Emma LU ; Malmström, Johan LU
; Keller, Ulrich Auf dem
; Walters, Marie
and Jacobsen, Stine
(2022)
In Osteoarthritis and Cartilage
30(1).
p.137-146
- Abstract
OBJECTIVE: The objectives of this study was to establish a sensitive and reproducible method to map the cartilage and subchondral bone proteomes in quantitative terms, and mine the proteomes for proteins of particular interest in the pathogenesis of osteoarthritis (OA). The horse was used as a model animal.
DESIGN: Protein was extracted from articular cartilage and subchondral bone samples from three horses in triplicate by pressure cycling technology or ultrasonication. Digested proteins were analysed by data independent acquisition based mass spectrometry. Data was processed using a pre-established spectral library as reference database (FDR 1%).
RESULTS: We identified to our knowledge the hitherto most comprehensive... (More)
OBJECTIVE: The objectives of this study was to establish a sensitive and reproducible method to map the cartilage and subchondral bone proteomes in quantitative terms, and mine the proteomes for proteins of particular interest in the pathogenesis of osteoarthritis (OA). The horse was used as a model animal.
DESIGN: Protein was extracted from articular cartilage and subchondral bone samples from three horses in triplicate by pressure cycling technology or ultrasonication. Digested proteins were analysed by data independent acquisition based mass spectrometry. Data was processed using a pre-established spectral library as reference database (FDR 1%).
RESULTS: We identified to our knowledge the hitherto most comprehensive quantitative cartilage (1758 proteins) and subchondral bone (1482 proteins) proteomes in all species presented to date. Both extraction methods were sensitive and reproducible and the high consistency of the identified proteomes (>97% overlap) indicated that both methods preserved the diversity among the extracted proteins. Proteome mining revealed a substantial number of quantifiable cartilage and bone matrix proteins and proteins involved in osteogenesis and bone remodeling, including ACAN, BGN, PRELP, FMOD, COMP, ACP5, BMP3, BMP6, BGLAP, TGFB1, IGF1, ALP, MMP3, and collagens. A number of proteins, including COMP and TNN, were identified in different protein isoforms with potential unique biological roles.
CONCLUSION: We have successfully developed two sensitive and reproducible non-species specific workflows enabling a comprehensive quantitative insight into the proteomes of cartilage and subchondral bone. This facilitates the prospect of investigating the molecular events at the osteochondral unit in the pathogenesis of OA in future projects.
(Less)
- author
- Bundgaard, Louise
LU
; Åhrman, Emma
LU
; Malmström, Johan
LU
; Keller, Ulrich Auf dem
; Walters, Marie
and Jacobsen, Stine
- organization
- publishing date
- 2022
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Osteoarthritis and Cartilage
- volume
- 30
- issue
- 1
- pages
- 137 - 146
- publisher
- W.B. Saunders
- external identifiers
-
- scopus:85116723412
- pmid:34547431
- ISSN
- 1063-4584
- DOI
- 10.1016/j.joca.2021.09.006
- language
- English
- LU publication?
- yes
- id
- e057d674-2836-4053-a512-3b09b5e48df6
- date added to LUP
- 2021-09-27 15:34:07
- date last changed
- 2025-05-04 22:30:05
@article{e057d674-2836-4053-a512-3b09b5e48df6,
abstract = {{<p>OBJECTIVE: The objectives of this study was to establish a sensitive and reproducible method to map the cartilage and subchondral bone proteomes in quantitative terms, and mine the proteomes for proteins of particular interest in the pathogenesis of osteoarthritis (OA). The horse was used as a model animal.</p><p>DESIGN: Protein was extracted from articular cartilage and subchondral bone samples from three horses in triplicate by pressure cycling technology or ultrasonication. Digested proteins were analysed by data independent acquisition based mass spectrometry. Data was processed using a pre-established spectral library as reference database (FDR 1%).</p><p>RESULTS: We identified to our knowledge the hitherto most comprehensive quantitative cartilage (1758 proteins) and subchondral bone (1482 proteins) proteomes in all species presented to date. Both extraction methods were sensitive and reproducible and the high consistency of the identified proteomes (>97% overlap) indicated that both methods preserved the diversity among the extracted proteins. Proteome mining revealed a substantial number of quantifiable cartilage and bone matrix proteins and proteins involved in osteogenesis and bone remodeling, including ACAN, BGN, PRELP, FMOD, COMP, ACP5, BMP3, BMP6, BGLAP, TGFB1, IGF1, ALP, MMP3, and collagens. A number of proteins, including COMP and TNN, were identified in different protein isoforms with potential unique biological roles.</p><p>CONCLUSION: We have successfully developed two sensitive and reproducible non-species specific workflows enabling a comprehensive quantitative insight into the proteomes of cartilage and subchondral bone. This facilitates the prospect of investigating the molecular events at the osteochondral unit in the pathogenesis of OA in future projects.</p>}},
author = {{Bundgaard, Louise and Åhrman, Emma and Malmström, Johan and Keller, Ulrich Auf dem and Walters, Marie and Jacobsen, Stine}},
issn = {{1063-4584}},
language = {{eng}},
number = {{1}},
pages = {{137--146}},
publisher = {{W.B. Saunders}},
series = {{Osteoarthritis and Cartilage}},
title = {{Effective protein extraction combined with data independent acquisition analysis reveals a comprehensive and quantifiable insight into the proteomes of articular cartilage and subchondral bone}},
url = {{http://dx.doi.org/10.1016/j.joca.2021.09.006}},
doi = {{10.1016/j.joca.2021.09.006}},
volume = {{30}},
year = {{2022}},
}