REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Sodium deoxycholate (SDC)	Sigma	Cat#30970
Tris (2-carboxyethyl) phosphine	Sigma	Cat#C4706
Chloroacetamide	Sigma	Cat#C0267
LysC	Wako	Cat#4548995075888
Trypsin	Promega	Cat#V5111
Acetonitrile	Sigma	Cat#75-05-8
25% LC-MS grade ammonia	Fisher chemical	Cat#533003
Trifluoroacetic acid	Sigma	Cat#76-05-1
Water, Optima L/MS Grade	Sigma	Cat#76-05-1
Deposited data
Proteomics Identifications Database (PRIDE)		PXD027597
Full analysis pipeline	https://github.com/klevdiamanti/multi-tissue_ms_proteomics
Software and algorithms
Cytoscape v3.7	Shannon et al., 2003
EnrichmentMap v3.3	Merico et al., 2010
AutoAnnotate v1.3.3	Kucera et al., 2016
limma v3.42.2	Ritchie et al., 2015
Camera	Wu et al., 2012
fgsea v1.12.0	Korotkevich et al., 2019
MaxQuant v1.6.0.1	Cox and Mann 2008
Andromeda	Cox et al., 2011
Spectronaut v13	Bruderer et al., 2015
Other
MSigDB v7.2 (19 September 2020)	Liberzon et al., 2011
UniProt	The UniProt Consortium, 2021
GO (from MSigDB v7.2)	Subramanian et al., 2005
GOslim (02 May 2020)	Mi et al., 2019
KEGG (from MSigDB v7.2)	Kanehisa et al., 2017
Reactome (from MSigDB v7.2)	Jassal et al., 2020
Empore SPE SDB-RPS disc	Sigma	Cat#66886-U
Reprosil-Pur Basic C18, 1.9μm	Dr. Maisch Gmbh	Cat#r119.b9
EASY-Nlc 1200 system	Thermo Fisher	Cat#LC140
Q Exactive™ HF-X Hybrid Quadrupole-Orbitrap™ Mass Spectrometer	Thermo Fisher	Cat#IQLAAEGAAPFALGMBFZ