PXD051182-1

PXD051182 is an original dataset announced via ProteomeXchange.

Title	Exploring the early molecular pathogenesis of osteoarthritis using differential network analysis of human synovial fluid
Description	This MS data set was used as validation data for an exploratory proteomics study of biomarkers in osteoarthritis (OA) using SOMAscan assay data. We analyzed human synovial fluid from three groups with the two methods: 1) deceased donors with mildly degenerated cartilage and/or meniscus, which is a well-known characteristic of OA, 2) deceased donors with no degeneration as controls and 3) total knee replacement patients with end-stage knee osteoarthritis. We conducted gaussian graphical network analyses of proteins from group 1 and 2 using SOMAscan assay data, and included the 800 aptamers/proteins with largest absolute log2 fold changes in the network construction. We found 102 differentially connected proteins, which of 31 were also present in the MS data set. After filtering out non-proteotypic peptides, proteins with only one peptide used for identification across all samples and proteins with more than 50% missing values, we ended up with 21 proteins. We analyzed these proteins by 1) estimating correlation between the methods on log2 standardized data sets and 2) compared log2 fold changes and 95%CIs by linear mixed effect model with quantification on the protein level as the outcome variable, adjusted for age and sex. Most proteins shown a positive correlation for the two methods. The comparison of log2 fold changes and 95%CIs between the methods show similar results for mild degeneration group when compared to healthy controls, whereas the results for the comparison between healthy controls and late stage OA group show dissimilarities for a few proteins. Shared first authors: Martin Rydén, Amanda Sjögren Authors: Patrik Önnerfjord, Aleksandra Turkiewicz, Jon Tjörnstrand* Last authors: Neserin Ali (neserin.ali@med.lu.se), Martin Englund (martin.englund@med.lu.se) Department of Clinical Sciences Lund, Lund University *Department of Orthopedics, Skåne University Hospital, Sweden
HostingRepository	PRIDE
AnnounceDate	2024-05-13
AnnouncementXML	Submission_2024-05-13_02:14:08.401.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amanda Sjögren
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-03 10:24:54	ID requested
⏵ 1	2024-05-13 02:14:08	announced
2	2024-10-22 06:38:58	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, osteoarthritis, synovial fluid

Patrik Onnerfjord
contact affiliation	Clinical Sciences Lund, Lund University
contact email	patrik.onnerfjord@med.lu.se
lab head
Amanda Sjögren
contact affiliation	Lund University
contact email	amanda.sjogren@med.lu.se
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/2024/05/PXD051182

PRIDE project URI

• PRIDE
  1. PXD051182
     1. Label: PRIDE project
     2. Name: Exploring the early molecular pathogenesis of osteoarthritis using differential network analysis of human synovial fluid