Table 1.

List of experiments

Experiment	Instrument	Treatment/labeling	Separation	Strain	Data contributors	Affiliation	Reference
gricat	LCQ Classic	ICAT	SCX	BY4741	J Ranish, T Ideker	ISB	[42]
cdc15_cdc23_newICAT	LCQ DECA	clICAT	SCX	BY4742	B Raught	ISB	-
cdc15_cdc23_oldICAT	LCQ DECA	ICAT	SCX	BY4742	B Raught	ISB	-
cdc15_cdc23_ICAT	LCQ DECA	clICAT	SCX	BY4742	B Raught	ISB	-
cdc23_amf_newICAT	LCQ DECA	clICAT	SCX	BY4742	B Raught	ISB	-
contFFE2Murea	LCQ DECA	clICAT	SCX	BY4741 ?	F Kregenow, R Aebersold	ISB	-
FFEY1	LCQ DECA	FFE	Unknown	BY4741 ?	F Kregenow, R Aebersold	ISB	-
FFEY1Scx	LCQ DECA	FFE	SCX	BY4741 ?	F Kregenow, R Aebersold	ISB	-
FFEY2	LCQ DECA XP	FFE	Unknown	BY4741 ?	F Kregenow, R Aebersold	ISB	-
PeteryeastIcatstdFFE	LCQ DECA XP	clICAT	Unknown	BY4741 ?	F Kregenow, R Aebersold	ISB	-
TSAAT000c	LCQ DECA XP	clICAT	SCX	BY2125	M Flory et al.	ISB	[43]
TSAAT030c	LCQ DECA XP	clICAT	SCX	BY2125	M Flory et al.	ISB	[43]
TSAAT060c	LCQ DECA XP	clICAT	SCX	BY2125	M Flory et al.	ISB	[43]
TSAAT090c	LCQ DECA XP	clICAT	SCX	BY2125	M Flory et al.	ISB	[43]
TSAAT120c	LCQ DECA XP	clICAT	SCX	BY2125	M Flory et al.	ISB	[43]
TSAAxT000old	LCQ DECA	ICAT	SCX	BY2125	M Flory	ISB	[43]
T00	LCQ DECA XP	ICAT	SCX	BY2125	M Flory	ISB	[43]
T30	LCQ DECA XP	ICAT	SCX	BY2125	M Flory	ISB	[43]
T50	LCQ DECA XP	ICAT	SCX	BY2125	M Flory	ISB	[43]
opd00034_YEAST	LCQ DECA XP	None	SCX	DBY8724	P Lu	University of Texas	[44]
opd00035_YEAST	LCQ DECA XP	None	SCX	DBY8724	P Lu	University of Texas	[44]
peroximalPrep0702	LCQ Classic	ICAT	SCX	BY4743	M Marelli et al.	ISB	[45]
Comp12vs12sizefrac	LCQ DECA	Iodoacetemide	SCX	BY4741	DB Martin	ISB	-
pxproteome	LCQ DECA	clICAT	SCX	BY4743	M Marelli et al.	ISB	[45]
Comp12vs12standSCX	LCQ DECA	Iodoacetemide	SCX	BY4741	DB Martin	ISB	-
YeastICAT	LCQ Classic	ICAT	SCX	Derivative of BY4741	J Ranish	ISB	-
PvM1	LCQ Classic	ICAT	SCX	BY4743	M Marelli et al.	ISB	[45]
peroximal_clICAT	LCQ Classic	clICAT	SCX	BY4743	M Marelli et al.	ISB	[45]
Ac30	LCQ DECA XP	clICAT	SCX	BY1782, BY2125	KR Serikawa et al.	University of Washington	[46]
yeast	LCQ DECA	Iodoacetemide	SCX	YPH499	Gygi et al.	Harvard Medical School	[47]
gel_msms	LCQ DECA	Iodoacetemide	Gel, SCX	BY4742	Ho et al.	MDS Proteomics	[30]
mudpit	LCQ DECA XP PLUS	Iodoacetemide	SDS-PAGE, SCX	YRP480	P Haynes et al.	University of Arizona	[48]
ipg_ief	LCQ DECA XP PLUS	Iodoacetemide	SDS-PAGE, IEF	YRP480	P Haynes et al.	University of Arizona	[48]
rp_int_selected	LCQ DECA XP PLUS	Iodoacetemide	SDS-PAGE	YRP480	P Haynes et al.	University of Arizona	[48]
rp_mass_selected	LCQ DECA XP PLUS	Iodoacetemide	SDS-PAGE	YRP480	P Haynes et al.	University of Arizona	[48]
sdspage	LCQ DECA XP PLUS	Iodoacetemide	SDS-PAGE	YRP480	P Haynes et al.	University of Arizona	[48]
YM_N14N15_DAYGly	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
YM_N14N15_DAYSer	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
YM_N14N15_SCYGly	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
YM_N14N15_SCYSer	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
APEX_04-22	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
APEX_04-23	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
APEX_04-24	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
APEX_04-28	LCQ Classic	None	Unknown	DBY8724	P Lu	University of Texas	[44]
YeastSCXReps	LCQ Classic	Iodacetimide	SCX	BY4741	Maynard et al.	NIH	[49]
FFE_nonICAT	LCQ Classic	Iodacetimide	FFE	BY2125?	Mingliang Ye	ISB

clICAT is acid cleavable ICAT D0227/D9236 and ICAT is the older ICAT reagent D0422/D8450. FFE, free flow electrophoresis; IEF, is isoelectric focusing; SCX, strong cation exchange; SDS-PAGE, sodium dodecyl (lauryl) sulfate-polyacrylamide gel electrophoresis.