REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-type I collagen	Millipore	Cat# AB765P; RRID: AB_92259
Goat polyclonal anti-type V collagen	Southern Biotech	Cat# 1350-01; RRID: AB_2794740
Mouse IgG1 monoclonal anti-skeletal muscle myosin heavy chain (MY32; clone MYSN02)	Thermo Fisher Scientific	Cat# MA5-11748; RRID: AB_10979315
Rat monoclonal anti-tenascin C (TNC; clone 578)	R & D Systems	Cat# MAB2138; RRID: AB_2203818
Rabbit polyclonal anti-fibrillin 2 (FBN2)	Gift from Dr. Robert Mecham	Beene et al.72
Mouse IgG1k monoclonal anti-nidogen-2 (NID2, clone F-2)	Santa Cruz Biotechnology	Cat# sc-377424; RRID: AB_2819357
Rabbit polyclonal anti-EMILIN1	Novus Biologicals	Cat# NBP1-84127; RRID: AB_11037041
Rat monoclonal perlecan (HSPG2; clone A7L6)	Santa Cruz Biotechnology	Cat# sc-33707; RRID: AB_627714
Alexa Fluor 488-conjugated goat anti-rabbit secondary antibody	Thermo Fisher Scientific	Cat# A-11034; RRID: AB_2576217
Alexa Fluor 488-conjugated donkey anti-rat secondary antibody	Thermo Fisher Scientific	Cat# A-21208; RRID: AB_2535794
Alexa Fluor 546-conjugated goat anti-mouse IgG1 secondary antibody	Thermo Fisher Scientific	Cat# A-21123; RRID: AB_2535765
Alexa Fluor 555-conjugated donkey anti-goat secondary antibody	Thermo Fisher Scientific	Cat# A-21432; RRID: AB_2535853
Alexa Fluor 633-conjugated goat anti-mouse IgG1 secondary antibody	Thermo Fisher Scientific	Cat# A-21126; RRID: AB_2535768
Alexa Fluor 647-conjugated donkey anti-rabbit secondary antibody	Thermo Fisher Scientific	Cat# A-31573; RRID: AB_2536183
Chemicals, peptides, and recombinant proteins
L-azidohomoalanine	Click Chemistry Tools	Cat#: 1066
Halt Protease Inhibitor Cocktail (100 $\times$)	Thermo Fisher Scientific	Cat#: 78429
Chondroitinase ABC from Proteus vulgaris	Sigma-Aldrich	Cat#: C3667
Diazo Biotin Alkyne	Click Chemistry Tools	Cat#: 1042
tris(3-hydroxypropyltriazolylmethyl)amine	Click Chemistry Tools	Cat#: 1010
Pierce NeutrAvidin Agarose	Thermo Fisher Scientific	Cat#: 29200
Endoproteinase LysC	New England Biolabs	Cat#: P8109S
Pierce Trypsin Protease, MS Grade	Thermo Fisher Scientific	Cat#: 90057
Pierce Detergent Removal Spin Columns	Thermo Fisher Scientific	Cat#: 87777
C-18 MicroSpin columns	The Nest Group, Inc.	Cat#: SS18V
Mouse on Mouse (MOM) Basic Kit	Vector Laboratories	Cat#: BMK-2202
ImmEdge Pen	Vector Laboratories	Cat#: H-4000
Fluoromount-G	SouthernBiotech	Cat#: 0100-01
Critical commercial assays
Compartment Protein Extraction Kit	Millipore EMD	Cat#: 2145
Pierce 660 nm Protein Assay	Thermo Fisher Scientific	Cat#: 22662
Pierce Quantitative Colorimetric Peptide Assay	Thermo Fisher Scientific	Cat#: 23275
Hydroxyproline Assay Kit	Sigma-Aldrich	Cat#: MAK008
MicroVue Bone PYD EIA	Quidel	Cat#: 8010
Deposited data
Mass spectrometry proteomics raw data	This paper	MassIVE: MSV000085556
Experimental models: Organisms/strains
Mus musculus: C57BL/6J (WT)	The Jackson Laboratory	Stock #: 000664
Mus musculus: B6C3Fe a/a-Col1a2oim/J (oim/oim)	The Jackson Laboratory	Stock #: 001815 Chipman et al.46
Software and algorithms
FIJI	Schindelin et al.73	RRID:SCR_002285
Illustrator	Adobe	v. 2019
Photoshop	Adobe	v. 2019
Excel	Microsoft	v. 2020
Prism	GraphPad	v. 8.3.1
MaxQuant	Cox et al.27,28	v. 1.6.1.0
g:Profiler	Reimand et al.76	RRID:SCR_006809
ENCODE	Dunham et al.77	https://www.encodeproject.org/
Gencode	Frankish et al.78	v. M27
nf-core RNA-seq pipeline	Ewels et al.79	v. 1.4.2
Other
TissueRuptor	Qiagen	https://www.qiagen.com/us
CentriVap Benchtop Vacuum Concentrator	Labconoco	https://www.labconco.com/
Branson Ultrasonics Sonifier S-450A	Fisher Scientific	Cat#: 22-309783
ThermoMixer, F1.5	Eppendorf	Cat#: 5384000020
Q Exactive™ HF Hybrid Quadrupole-Orbitrap Mass Spectrometer	Thermo Fisher Scientific	Cat#: IQLAAEGAAPFAALGMBFZ
Shandon Cryotome FE	Thermo Fisher Scientific	Cat#: A78910100
Leica DMI6000 Microscope	Leica Microsystems	https://www.leica-microsystems.com/