'GENE_NAME' refers to commonly used gene symbols.		
		
'PROTEIN_ID' refers to the Uniprot identifiers.		
		
"The remaining columns list samples assayed by TMT-based proteomics. Three biological replicates were assayed for MCF10A (designated 'MCF10A_REP1', 'MCF10A_REP2', and 'MCF10A_REP3'). Two biological replicates were assayed for EFM19 (designated as 'EFM19_REP1' and 'EFM19_REP2'), ZR7530 (designated as 'ZR7530_REP1' and 'ZR7530_REP2'), ZR751 (designated as 'ZR751_REP1' and 'ZR751_REP2'), 184A1 (designated as '184A1_REP1' and '184A1_REP2'), and EVSAT (designated as 'EVSAT_REP1' and 'EVSAT_REP2'). The cell lines were as follows:"		
		
Cell Line	HMS LINCS ID	Notes
184A1	51088-1	2 biological replicates
184B5	50576-2	
AU565	50091-3	
BT-474	50106-2	
BT-483	50107-2	
EFM-19	51113-1	2 biological replicates
EVSA-T	51138-1	2 biological replicates
HCC1187	50578-2	
HCC1569	50210-2	
HCC202	50214-2	
MCF 10A	50583-4	3 biological replicates
MCF12A	51089-2	
MDA-MB-175-VII	50329-2	
MDAMB330	51139-1	
MDA-MB-415	50332-1	
MGH312	51140-1	
MGH358	51141-1	
PDX1206	51137-1	
SUM185PE	51084-1	
SUM190PT	51121-1	
SUM229PE	51086-1	
SUM44PE	51122-1	
SUM52PE	51087-1	
UACC-812	50556-2	
UACC-893	50557-2	
ZR-75-1	50574-2	2 biological replicates
ZR-75-30	50575-1	2 biological replicates
		
		
"Columns labeled 'NEW BRIDGE5', 'OLD BRIDGE5', 'NEW BRIDGE6', 'BRIDGE7', 'OLD BRIDGE8', and 'NEW BRIDGE8' refer to:"		
		
Pooled samples of 6 cell lines used to normalize the data across batches.		
