REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
sodium dodecyl sulfate	Sigma	Cat#L4509-10G
protease inhibitor cocktail	Sigma	Cat#P2714
PhosphoSTOP	Roche	Cat#04906837001
LysC	Wako	Cat#125-05061
Trypsin	Thermo Fisher	Cat#90057
Bio-Rad Protein Assay Kit – BSA	Bio-rad	Cat#5000002
Amicon Ultra MWCO 10K filters	Millipore	Cat#UFC501096
HLB 1cc (10 mg) extraction cartridges	Oasis	Lot#149A37130B
TiO2 phosphopeptide enrichment spin tips	Thermo Fisher	Cat#88303
Deposited data
Phosphorylation - Mass Spectrometry data	PRIDE repository	PXD044648
Protein Expression - Mass Spectrometry data (data from previous study)	PRIDE repository	PXD030161
Experimental models: Organisms/strains
5XFAD mice (B6SJL-Tg(APPSwFlLon, PSEN1∗M146L∗L286V) 6799Vas/Mmjax)	Jackson Laboratories	RRID:MMRRC_034840-JAX
WT mice (C57BL/6J)	Jackson Laboratories	RRID:IMSR_JAX:000664
Software and algorithms
AD-Xplorer	https://yilmazs.shinyapps.io/ADXplorer	https://github.com/serhan-yilmaz/AD-Xplorer
Self-contained package (code and data) to reproduce the analysis results	Figshare	https://doi.org/10.6084/m9.figshare.23903715
Other
NanoAcquity UPLC chromatography	Waters	176016000
Thermo Scientific Orbitrap Elite mass spectrometer	Thermo Fisher	FSN40129