PXD038207

PXD038207 is an original dataset announced via ProteomeXchange.

Title	Robust and Highly Efficient Extractions of Proteins from Bones enable Deep, High-Throughput Proteomic Quantification to Gain Insights into Bone Biology
Description	Dysregulation of cell signaling in bone cells, such as osteocytes, osteoblasts, osteoclasts, and chondrocytes, and elevated burden of senescent cells in bone and cartilage, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides a crucial molecular tool-kit to understand complex signaling relationships in age-related diseases, such as OA. Here we introduce a novel mass spectrometric workflow to promote proteomic studies of bone and cartilage. This workflow uses highly specialized steps, including extensive overnight demineralization, pulverization, and incubation for 72 h in 6 M guanidine hydrochloride and EDTA, followed by proteolytic digestion. Analysis on a high-resolution Orbitrap Eclipse and Orbitrap Exploris 480 mass spectrometer using Data-Independent Acquisition (DIA) provides deep coverage of the bone proteome, and preserves post-translational modifications, such as hydroxyproline. A spectral library-free quantification strategy, directDIA, identified and quantified over 2,000 protein groups (with more than 2 unique peptides) from calcium-rich bone matrices. Key components identified were proteins of the extracellular matrix (ECM), bone-specific proteins (e.g., bone sialoprotein 2, IBSP), and signaling proteins (e.g., transforming growth factor beta-2, TGFB2) and lysyl oxidase homolog 2 (LOXL2), an important protein in collagen crosslinking. Post-translational modifications (PTMs) were identified without the need for specific enrichment. This includes collagen hydroxyproline modifications, chemical modifications for collagen self-assembly and network formation. Multiple senescence factors were identified, such as C3 protein of the complement system and many matrix metalloproteinases, that might be monitored during age-related bone disease progression. Our innovative workflow yields in-depth protein coverage and quantification strategies to discover underlying biological mechanisms of bone aging and to provide tools to monitor therapeutic interventions.
HostingRepository	MassIVE
AnnounceDate	2023-09-27
AnnouncementXML	Submission_2023-09-27_10:08:53.463.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacob Rose
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Oxidation
Instrument	Orbitrap Exploris 480; Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-17 16:30:54	ID requested
⏵ 1	2023-09-27 10:08:53	announced

no publication

submitter keyword: Bone Proteomics, Proteomics, DIA-MS, Aging, Senescence

Birgit Schilling
contact affiliation	Buck Institute
contact email	bschilling@buckinstitute.org
lab head
Jacob Rose
contact affiliation	Buck Institute
contact email	jrose@buckinstitute.org
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000090737/