REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Phospho-Bad antibody (Ser155) (rabbit polyclonal)	Cell Signaling	Cat# 9297; RRID:AB_2062131
Phospho-PKA Substrate antibody (RRXS∗/T∗) (clone 1000G7E) (rabbit monoclonal antibody)	Cell Signaling	Cat# 9624; RRID:AB_331817
Phospho-IKKB antibody (Ser672) (rabbit polyclonal)	Aviva Systems Biology	Cat# OAAB16292
IKK-beta antibody (clone 10AG2) (mouse monoclonal)	Millipore	Cat# 05-535; RRID:AB_2122161
Phospho-MST2 antibody (Ser316) (rabbit polyclonal)	Invitrogen	PA-105065
MST2 antibody (rabbit polyclonal)	Cell Signaling	Cat# 3952; RRID:AB_2196471
Phospho-MCM2 antibody (Ser139) (clone D1Z8X) (rabbit monoclonal)	Cell Signaling	Cat#12958; RRID:AB_2798069
MCM2 antibody (clone D7G11) XP(R) (rabbit monoclonal)	Cell Signaling	Cat# 3619; RRID:AB_2142137
Phospho-S6 antibody (Ser235/326) (rabbit polyclonal)	Cell Signaling	Cat# 2211; RRID:AB_331679
S6 ribosomal protein antibody (clone 54D2) (mouse monoclonal)	Cell Signaling	Cat# 2317; RRID:AB_2238583
β-actin antibody (clone C4) (mouse monoclonal)	Santa Cruz	Cat#: sc-47778; RRID:AB_626632
Anti-rabbit IgG, HRP-linked antibody	Cell Signaling	Cat#7074; RRID:AB_2099233
Anti-mouse IgG, HRP-linked antibody	Cell Signaling	Cat#: 7076; RRID:AB_330924
Chemicals, peptides, and recombinant proteins
Ammonium Acetate	Sigma Aldrich	Cat# A7330
RIPA buffer	Thermo Fisher	Cat# 89901
Forskolin, Coleus forskohlii in DMSO	EMD Millipore	Cat# 344282
H-89, Dihydrochloride	EMD Millipore	Cat# 371962
Deposited data
Hyperammonemia-dependent and independent skeletal muscle phosphoproteomic responses during exercise	This paper	ProteomeXchange: PXD031372
Mitochondrial responses during hyperammonemia	ProteomeXchange	ProteomeXchange: PXD026955
Transcriptomic, proteomic and phosphoproteomic underpinnings of daily exercise performance and Zeitgeber activity of endurance training in mouse skeletal muscle	ProteomeXchange	ProteomeXchange: PXD026461
The exercise-regulated skeletal muscle phosphoproteome	ProteomeXchange	ProteomeXchange: PXD001543
Phosphoproteomic screening of exercise-like treatments reveals drug interactions regulating protein secretion	ProteomeXchange	ProteomeXchange: PXD014322
Phosphoproteomics of rodent exercise models	ProteomeXchange	ProteomeXchange: PXD010452
Impact of maximal-intensity contractions and rapamycin on the proteome and phosphoproteome of mouse skeletal muscle	University of California San Diego (UCSD) MassIVE Database	MassIVE database: MSV000086732
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [ATAC-seq]	GEO	GSE171642
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [human RNA-seq]	GEO	GSE171643
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [mouse RNA-seq]	GEO	GSE171644
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia	GEO	GSE171645
Experimental models: Cell lines
C2C12 myotubes	ATCC	CRL-1772
Software and algorithms
IPA	QIAGEN, Inc.	https://digitalinsights.qiagen.com/IPA
g:Profiler	N/A	https://biit.cs.ut.ee/gprofiler/gost
RStudio	N/A	Rstudio.com
ImageJ	NIH	https://imagej.nih.gov/ij/
Perseus	MaxQuant	https://maxquant.net/perseus/
Phomics	N/A	http://phomics.jensenlab.org/phospho_enrichment
STRING	String Consortium 2022	https://string-db.org/
Other
Phosphoproteomics Scatterplot code	Zenodo and GitHub	v0.1SitesPerProtein dasaraslab/Unbiased: Phosphoproteomics Scatterplot https://zenodo.org/badge/latestdoi/392334492