Table 1. Chicken utricle hair bundle proteins.

Proteins were listed if they were (a) identified in at least three of five experiments (see Suppl. Table 1), (b) had a log(e) of -20 or better in at least one experiment, and (c) had a total spectral count of 3 or more in at least one experiment. Key: Rank IF, rank order based on intensity factor (IF); Rank SCF, rank order based on spectral counting (spectral count factor; SCF); Identifier, Chicken Ensembl database reference identifiers; #, number of mass spectrometry experiments protein was identified in; Best log(e), lowest log(e) score for protein; Best count, largest spectral count for protein; MW (kDa), molecular mass in kDa; IF, intensity factor score; SCF, spectral count factor score; Name, descriptive name, with chicken gene name indicated in some cases.

Rank, IF	Rank, SCF	Identifier	#	Best log(e)	Best count	MW (kDa)	IF	SCF	Name
1	1	ENSGALP00000002101	5	−573.9	259	41.8	0.3373	0.2789	Beta-actin (ACT5_CHICK)
2	2	ENSGALP00000018742	5	−296.2	107	42.9	0.0651	0.0543	Creatine kinase B (KCRB_CHICK)
3	3	ENSGALP00000023278	5	−291.7	44	35.7	0.0406	0.0345	Glyceraldehyde-3-phosphate dehydrogenase (G3P_CHICK)
4	4	ENSGALP00000005475	4	−101.3	29	12.1	0.0297	0.0324	Parvalbumin 3 (PRVU_CHICK)
5	10	ENSGALP00000016260	3	−37.5	7	16.8	0.0152	0.0142	Calmodulin (CaM)
6	7	ENSGALP00000010510	5	−239.6	45	70.8	0.0145	0.0157	Heat shock cognate 70
7	5	ENSGALP00000013964	5	−190.0	38	43.5	0.0139	0.0166	Tubulin beta-2C (TUBB2C)
8	8	ENSGALP00000021618	5	−66.1	25	36.3	0.0132	0.0157	L-lactate dehydrogenase B (LDHB_CHICK)
9	18	ENSGALP00000017577	4	−30.1	11	19.1	0.0129	0.0098	Anterior gradient homolog (AG-3 protein)
10	9	ENSGALP00000026911	5	−140.4	19	28.2	0.0125	0.0142	Chloride intracellular channel protein 5 (CLIC5)
11	14	ENSGALP00000019165	4	−37.6	6	12.2	0.0118	0.0118	Histone H4
12	6	ENSGALP00000023396	4	−77.7	15	22.7	0.0114	0.0166	Triosephosphate isomerase (TPIS_CHICK)
13	11	ENSGALP00000027650	5	−162.5	36	68.4	0.0113	0.0133	Radixin (RADI_CHICK)
14	20	ENSGALP00000019162	3	−33.2	6	15.6	0.0102	0.0095	Histone H2A
15	13	ENSGALP00000019365	5	−111.0	15	37.5	0.0094	0.0120	Annexin A5
16	15	ENSGALP00000016978	4	−202.6	31	50.8	0.0090	0.0109	Tubulin alpha-1 (TBA1_CHICK)
17	22	ENSGALP00000011961	3	−49.9	14	20.9	0.0090	0.0090	Phosphatidylethanolamine-binding protein (PEBP)
18	17	ENSGALP00000003737	5	−197.7	30	50.2	0.0086	0.0101	Alpha-enolase (ENO1)
19	19	ENSGALP00000004164	5	−166.4	27	70.9	0.0085	0.0097	Fimbrin (FIMB_CHICK)
20	16	ENSGALP00000003012	4	−101.5	18	35.6	0.0079	0.0102	Malate dehydrogenase mitochondrial (MDH)
21	21	ENSGALP00000008988	5	−121.2	19	39.0	0.0075	0.0093	NHERF1
22	12	ENSGALP00000012878	4	−149.7	22	44.6	0.0072	0.0127	Phosphoglycerate kinase (PGK_CHICK)
23	24	ENSGALP00000004703	4	−20.3	7	19.3	0.0063	0.0068	Ubiquitin (UBIQ_CHICK)
24	26	ENSGALP00000003665	3	−20.4	4	12.7	0.0059	0.0059	Calretinin (CALB2)
25	25	ENSGALP00000014374	5	−62.6	10	36.5	0.0056	0.0064	Malate dehydrogenase cytoplasmic
26	29	ENSGALP00000008647	3	−21.5	10	20.7	0.0056	0.0056	ADP-ribosylation factor 1 (ARF1)
27	23	ENSGALP00000004182	4	−35.9	10	29.2	0.0054	0.0086	14-3-3 protein epsilon (14-3-3E)
28	31	ENSGALP00000001474	4	−106.4	22	72.0	0.0054	0.0054	GRP 78/BiP (GRP78_CHICK)
29	28	ENSGALP00000016523	4	−83.4	33	83.4	0.0049	0.0057	Heat shock protein HSP 90-beta (HS90B_CHICK)
30	35	ENSGALP00000016629	3	−40.5	8	22.3	0.0047	0.0047	Peroxiredoxin 1
31	27	ENSGALP00000034108	4	−117.7	18	58.0	0.0045	0.0058	Pyruvate kinase muscle isozyme (KPYK_CHICK)
32	30	ENSGALP00000002695	5	−111.9	13	60.6	0.0042	0.0054	ATP synthase H+ transporting mitochondrial F1 alpha
33	40	ENSGALP00000018498	3	−65.8	25	64.6	0.0039	0.0039	Heat shock protein HSP 90-alpha (Q5ZIC0_CHICK)
34	37	ENSGALP00000017765	5	−141.8	22	86.4	0.0038	0.0043	EPLIN (epithelial protein lost in neoplasm)
35	34	ENSGALP00000017773	5	−309.2	51	257.2	0.0036	0.0049	Protein tyrosine phosphatase RQ (PTPRQ)
36	42	ENSGALP00000032508	3	−33.4	7	27.7	0.0035	0.0035	Glutathione transferase omega
37	32	ENSGALP00000025499	4	−28.1	3	15.7	0.0034	0.0050	Superoxide dismutase
38	36	ENSGALP00000018265	4	−64.2	7	24.4	0.0034	0.0045	47 kDa heat shock protein (HSP47_CHICK)
39	33	ENSGALP00000010167	4	−53.0	9	42.1	0.0033	0.0050	L-lactate dehydrogenase A (LDHA_CHIC)
40	39	ENSGALP00000025573	4	−258.7	34	147.5	0.0032	0.0042	Myosin VI
41	38	ENSGALP00000013574	4	−93.3	13	50.4	0.0032	0.0043	Protein disulfide-isomerase A3
42	44	ENSGALP00000020744	4	−113.5	15	92.3	0.0024	0.0029	GRP94 (endoplasmin) (ENPL_CHICK)
43	43	ENSGALP00000020268	5	−61.3	13	73.3	0.0024	0.0031	Protein disulfide isomerase family A member 4
44	45	ENSGALP00000007934	3	−98.5	12	62.1	0.0022	0.0022	Glucose phosphate isomerase
45	48	ENSGALP00000007997	3	−26.2	5	31.2	0.0020	0.0020	Voltage-dependent anion-selective channel protein 2 (VDAC-2)
46	41	ENSGALP00000026461	3	−22.0	4	28.7	0.0020	0.0037	14-3-3 protein theta (14-3-3T)
47	47	ENSGALP00000000304	4	−95.3	13	73.4	0.0018	0.0022	Dihydropyrimidinase-related protein 2 (DRP-2)
48	46	ENSGALP00000013267	4	−63.1	9	49.5	0.0016	0.0022	GDP dissociation inhibitor 2
49	51	ENSGALP00000014371	3	−44.6	8	95.1	0.0015	0.0015	Novel Ensembl prediction
50	52	ENSGALP00000007703	3	−145.0	16	137.1	0.0012	0.0014	Plasma membrane Ca2+ ATPase 2 (ATP2B2)
51	49	ENSGALP00000011689	3	−36.0	5	44.1	0.0012	0.0019	Protein disulfide isomerase
52	50	ENSGALP00000009371	3	−41.6	5	50.5	0.0011	0.0016	Elongation factor 1-alpha 2 (EF-1-alpha-2)
53	53	ENSGALP00000003850	3	−23.1	3	57.8	0.0010	0.0010	T-complex protein 1 zeta-2 subunit
54	54	ENSGALP00000025506	3	−21.6	3	64.5	0.0009	0.0009	Malic enzyme 1 NADP(+)-dependent cytosolic
55	55	ENSGALP00000017926	3	−26.7	6	62.4	0.0009	0.0009	Phosphoglucomutase 1
56	56	ENSGALP00000018987	3	−25.4	4	61.0	0.0009	0.0009	T-complex protein 1 alpha subunit (TCP-1-alpha)
57	57	ENSGALP00000011233	3	−36.7	5	86.8	0.0008	0.0008	6-phosphofructokinase type C
58	58	ENSGALP00000002625	3	−37.5	3	56.8	0.0006	0.0006	Vacuolar H-ATPase B subunit osteoclast isozyme
59	59	ENSGALP00000008236	3	−102.2	13	192.2	0.0004	0.0006	Clathrin heavy chain