REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human skeletal muscle biopsies	This paper	N/A
Chemicals, peptides and recombinant proteins
UREA	Sigma Aldrich	Cat#U5378
Ammonium bicarbonate, NH4HCO3	Sigma Aldrich	Cat#A6141
Tris(2-carboxyethyl)phosphine	Sigma Aldrich	Cat#C4706
Iodoacetamide	Fluka BioChemica	Cat#57670
Sequencing Grade Modified Trypsin	Promega	Cat#V5113
Formic acid	Fluka	Cat#56302-10X1ML
Acetonitrile	Merck	Cat#1000292500
Trifluoroacetic acid	Fluka	Cat#40967-10x1ml
10% ammonia	Fluka	Cat#17837
Critical commercial assays
BCA protein assay kit	Pierce, Thermo Scientific	Cat#23225
iRT-peptide kit	Biognosys	Ki-3002-2
Software and algorithms
SPSS Statistics	IBM	version 25
RStudio	RStudio Team https://www.rstudio.com/	RStudio version 1.4.1106
R	R Core Team https://www.r-project.org/	R version 4.0.54
ProteinPilot software	AB SCIEX	Paragon algorithm (v4.5)
PeakView	AB SCIEX	version 2.1 with SWATH quantitation plug-in
MaxQuant	Cox and Mann. 2008	version 1.6.0.16
Human Uniprot Database	www.uniprot.org	release 11_2018 with 20,347 entries
Human Uniprot Database	www.uniprot.org	release 01_2020 with 20,303 entries
DAVID bioinformatics resources	https://david.ncifcrf.gov/	version 6.8
VENNY 2.1	https://bioinfogp.cnb.csic.es/tools/venny/	version 2.1
PhosphoSitePlus®	www.phosphosite.org	version 6.5.9.3
NetworKIN software	Horn et al., 2014	version 2.1
Other
FastPrep-24 5G bead homogenizer	MP Biomedicals	116005500
Agilent 3100 OFFGEL fractionator	Agilent Technologies	RRID:SCR_019388
TripleTOF® 6600 Quadrupole Time-Of-Flight instrument	Sciex	TripleTOF 6600
Eksigent nanoLC with a Turbo V Source	Sciex	Turbo V Source
Q Exactive ESI-quadrupole-orbitrap mass spectrometer	Thermo Fisher Scientific	RRID:SCR_020571
EASY-nLC 1000 nanoflow LC	Thermo Fisher Scientific	RRID:SCR_014993
zirconia beads	BioSpec Products	1 mm beads
IPG strips	GE Healthcare	24 cm pH 3–10
C18 microspin columns	Nest Group	HUM S18V
YMC-Triart C18 column	YMC	12nm, 3μm, 150x0.3mm
Acclaim PepMap™100	Thermo Fisher Scientific	100 μm×2cm, 3μm, 100Å
Acclaim PepMap™100	Thermo Fisher Scientific	75 μm×15cm, 2μm, 100Å