Table 2. Proteins Identified in Anti-YFP Immunoprecipitates from Two Independent Lines Overexpressing FtsH12-YFP.

Accession No.	Identified Proteins (236/247)	PUBQ10:FtsH12-YFP
		1	2
AT1G79560	FtsH protease 12, Embryo defective 1047, Embryo defective 156, Embryo defective 36	386	371
ATCG00860	Chloroplast Ycf2	181	237
AT3G04340	FtsH extracellular protease family, FtsHi 5, Embryo defective2458	247	179
ATCG01130	Chloroplast Ycf1, TIC214	70	111
AT3G16290	FtsH extracellular protease family, FtsHi 2, Embryo defective 2083	46	86
AT5G64580	FtsH extracellular protease family, FtsHi 4, Embryo defective 3144	66	83
AT4G23940	FtsH extracellular protease family, ARC1, FtsHi1	69	52
AT1G01320	Tetratricopeptide repeat-like superfamily protein	6	32
AT4G02510	Translocon at the outer envelope membrane of chloroplasts 159	37	31
AT5G53860	Embryo defective 2737	13	26
ATCG00480	ATP synthase subunit beta	8	23
AT3G47520	pdNAD-MDH	5	22
AT1G07920	GTP binding Elongation factor Tu family protein	15	20
AT1G43170	Ribosomal protein 1	5	20
ATCG00120	ATP synthase subunit alpha	42	19
ATCG00490	Ribulose-bisphosphate carboxylase	48	16
AT5G01590	Histone-lysine N-methyltransferase ATXR3-like protein	14	16
AT2G41840	Ribosomal protein S5 family protein	6	16

The IPs were conducted with anti-YFP beads on extracts of material harvested from rosette leaves, and the coeluting proteins were identified using LC-MS/MS. Values represent the total spectrum count of peptides matching each protein. Proteins found in the control sample (IPs from wild-type plants) were assumed to be contaminants and excluded. The full data set can be found in Supplemental Data Set 1.