Table 2.

Identification of ERβ-interacting proteins in H1793 and A549 cells by LC-MS/MS.

	Cell line/treatment Protein name	gene name	HPRD		Tarallo et al [40]
			ERβ	ERα	ERβ	ERα
	H1793, EtOH
1	Tubulin beta-2A chain	TUBB2A
2	Myosin-9	MYH9				+
3	β-actin	ACTB			+	+
4	Tubulin alpha-3C/D chain	TUBA3C
5	Vimentin	VIM			+
6	ERβ	ESR2	+		+
7	Heat shock 70 kDa (Hsp70)	HSPA8		+	+	+
8	Histone H2A type 1-H	HIST1H2
9	Heat shock 60 kDa (Hsp60)	HSPD1				+
10	Putative annexin A2-like protein	ANX2P2
11	40S ribosomal protein S3	RPS3			+
12	Protein arginine N-methyltransferase 5	PRMT5		+
13	Calmodulin	CALM	+			+
14	Histone H4	HIST1H4A			+
15	GTP-binding nuclear protein	RAN
	H1793, E2
1	β-actin	ACTB			+	+
2	Myosin-9	MYH9				+
3	Tubulin beta-2A chain	TUBB2A
4	Tubulin alpha-3C/D chain	TUBA3C		+
5	Tropomyosin alpha-4 chain	TPM3
6	60 kDa heat shock protein	HSPD1				+
7	Histone H2A type 1-H	HIST1H2			+
8	Heat shock 70 kDa protein 1-like	HSPA8		+	+
9	Vimentin	VIM			+
10	Nucleolin	NCL				+
11	Tropomyosin alpha-3 chain	TPM3
12	Nucleophosmin	NPM1				+
13	Myosin-VI	MYO6				+
14	Plectin	PLEC
15	40S ribosomal protein S3	RPC3			+
16	60S ribosomal protein	RPL8				+
17	Heterogeneous nuclear ribonucleoproteins A2/B1	HNRNPA2
	A549, EtOH
1	Tubulin beta-2A chain	TUBB2A
2	Actin	ACTB			+
3	Tubulin alpha-3C/D chain	TUBA3C		+
4	Heat shock 70 kDa protein	HSPA8		+	+	+
5	60 kDa heat shock protein	HSPD1				+
6	Histone H2A type 1-H	HIST1H2			+
7	40S ribosomal protein S3	RPC3			+
8	Histone H4	HIST1H2A			+
9	Tropomyosin alpha-1 chain	TPM1
10	Myosin-9	MYH9
11	Calmodulin	CALM	+
12	Myosin regulatory light chain 12A	MYL12A
	A549, E2
1	Tubulin beta-2A chain	TUBB2A
2	Actin	ACTB			+
3	Tubulin alpha-3C/D chain	TUBA3C		+
4	Heat shock 70 kDa protein	HSPA8		+	+
5	Myosin-9	MYH9				+
6	40S ribosomal protein S3	RPC3			+
7	60 kDa heat shock protein	HSPD1				+
8	Histone H4	HIST1H2A			+
9	Elongation factor 1-alpha 1	EEF1A1				+
10	Calmodulin	CALM	+
11	Tropomyosin alpha-1 chain	TPM1
12	40S ribosomal protein S23	RPC23

H1793 and A549 cells were treated for 1 h with EtOH (vehicle) or 10 nM E₂ and FLAG-ERβ-interacting proteins were immunocaptured, eluted, and trypsin-digested as described in Additional file 1, Figure S1. Trypsin-digested eluates were subjected to LC-MS/MS peptide identification (see Additional file 4, Table S2). Proteins are listed from highest to lowest score within each cell line/treatment group. The literature citations for previous identification of these proteins as interacting with ERβ and ERα are provided from the Human Protein Reference Database (HPRD, www.hprd.org) databases and Tarallo et al. [40].