KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical Commercial Assays
Tandem Mass Tag (TMT) Reagents, 10plex, 11plex, and 16plex sets	Thermo Fisher Scientific	Cat# 90110 Cat# A34808 Cat# A44521
Chemicals, Peptides, and Recombinant Proteins
cOmplete, Mini Protease Inhibitor Cocktail	Sigma-Aldrich	Cat# 11836153001
PhosSTOP Phosphatase Inhibitor Tablets	Sigma-Aldrich	Cat# 04906837001
XL188	Sara Buhrlage, Dana Farber Cancer Institute (DFCI) (Lamberto et al., 2017)	N/A
XL203C	Sara Buhrlage, DFCI (Lamberto et al., 2017)	N/A
XL177A	Sara Buhrlage, DFCI (Schauer et al., 2020)	N/A
XL177B	Sara Buhrlage, DFCI (Schauer et al., 2020)	N/A
P22077	Sara Buhrlage, DFCI (Altun et al., 2011)	N/A
GNE-6640	Sara Buhrlage, DFCI (Kategaya et al., 2017)	N/A
AZ1	Sara Buhrlage, DFCI (Wrigley et al., 2017)	N/A
SB1-B-55	Sara Buhrlage, DFCI (Guerin et al., 2017)	N/A
SB1-F-70	Sara Buhrlage, DFCI (Stockley, Kemp and Madin, 2018)	N/A
SB1-F-78	Sara Buhrlage, DFCI (Stockley, Kemp and Madin, 2018)	N/A
ML323	Sara Buhrlage, DFCI (Dexheimer et al., 2010)	N/A
WH-9943-91	Sara Buhrlage, DFCI (Buckmelter et al., 2017)	N/A
Deposited Data
wp-esf_038	This paper	PXD020873
wp-esf_039	(Donovan et al., 2018)	PXD010428
wp-esf_061	This paper	PXD020881
wp-esf_098	This paper	PXD020882
wp-esf_194	This paper	PXD020865
Experimental Models: Cell Lines
MM.1S (H. sapiens)	ATCC	CRL-2974; RRID: CVCL_8792
Software and Algorithms
Proteome Discoverer 2.2	Thermo Fisher Scientific	RRID: SCR_014477
R Framework	(R Core Team, 2019)	http://www.R-project.org/
Limma Package (R framework)	(Ritchie et al., 2015)	https://doi.org/doi:10.18129/B9.bioc.limma