. 2015 Dec 1;12(6):398–407. doi: 10.1089/zeb.2015.1121

Table 1.

Significantly Enriched Proteins Identified by Combined Mascot and SEQUEST Database Searches and Combined Spectral Counting and MS² TIC Features Generated in Scaffold 4 Software Comparing Deyolked and Nondeyolked Control Zebrafish Embryos

Protein name	Accession number	Molecular weight (kDa)	Student's t-test or G-test^a(p < 0.05)	Yolk average: total MS² TIC or spectral counts^b	Deyolked average: total MS² TIC or spectral counts^b
Aconitase 2, mitochondrial^c	F8W4M7_DANRE	86	0.002	Not identified without deyolking	1.70E+04 ± 2.34E+03
Actin, alpha 1, skeletal muscle^d	Q9I8V1_DANRE	42	0.008	1.92E+06 ± 2.52E+05	4.20E+06 ± 3.86E+05
Actinodin 2^c	A9JRX1_DANRE	57	0.037	Not identified without deyolking	1.59E+04 ± 5.16E+03
Adenosine monophosphate deaminase 1 (Isoform M)^c,e	Q6P3G5_DANRE	83	0.045	Not identified without deyolking	5.43E+04 ± 1.88E+04
Adenylate kinase isoenzyme 1^c,e	Q68EH2_DANRE	21	0.030	4.69E+04 ± 1.48E+04	1.02E+05 ± 8.06E+03
ATP synthase subunit alpha^d	Q08BA1_DANRE	60	<0.001	8.32E+04 ± 4.65E+03	3.71E+05 ± 1.02E+04
ATP synthase subunit beta^d	F1R2V7_DANRE	56	0.001	Not identified without deyolking	3.75E+05 ± 4.71E+04
ATPase, H⁺ transporting, lysosomal, V1 subunit Ab^c,e	E7FCD8_DANRE	68	0.005	Not identified without deyolking	2.94E+05 ± 5.26E+04
BetaA2-2-crystallin^c,e	Q45FX9_DANRE	24	0.015	Not identified without deyolking	4.97E+03 ± 1.21E+03
Brain-subtype creatine kinase^c,e	Q8AY63_DANRE	43	0.012	Not identified without deyolking	1.82E+05 ± 4.15E+04
Calsequestrin^c,e	F1QNI9_DANRE	32	0.018	Not identified without deyolking	8.68E+04 ± 2.24E+04
	F1QXT6_DANRE
Clathrin heavy chain^c,e	F1R966_DANRE	192	0.012	Not identified without deyolking	4.91E+04 ± 1.12E+04
Creatine kinase, mitochondrial 2 (Sarcomeric)^c,e	Q6PC86_DANRE	46	0.036	Not identified without deyolking	2.02E+04 ± 6.49E+03
Creatine kinase, muscle a^d	A2BHA3_DANRE	43	0.007	Not identified without deyolking	6.30E+05 ± 1.22E+05
Creatine kinase, muscle b^d	Q7T306_DANRE	43	0.004	Not identified without deyolking	2.53E+05 ± 4.26E+04
Crystallin, beta B1^c	F1QT01_DANRE	29	0.041	Not identified without deyolking	5.63E+04 ± 1.89E+04
Dachsous cadherin-related 1a^c,e	F1R256_DANRE	352	0.004	2.26E+04 ± 2.26E+04	1.64E+05 ± 5.81E+03
	X1WDW2_DANRE
Elongation factor 1-gamma^c	EF1G_DANRE	50	0.001	Not identified without deyolking	5.85E+04 ± 7.10E+03
Epiphycan^c	B0S5X0_DANRE	75	<0.001	Not identified without deyolking	8.00E+04 ± 4.24E+03
	Q5RI46_DANRE
Fast skeletal muscle myosin light polypeptide 3^c	Q9I8U7_DANRE	17	0.014	7.23E+05 ± 1.19E+05	1.48E+06 ± 1.34E+05
Fructose-bisphosphate aldolase^c	Q803Q7_DANRE	40	0.025	Not identified without deyolking	5.98E+03 ± 1.70E+03
GDP dissociation inhibitor 2^c,e	Q6TNT9_DANRE	51	0.007	Not identified without deyolking	6.23E+04 ± 1.23E+04
Glyceraldehyde-3-phosphate dehydrogenase^d	F1R3D3_DANRE	36	0.001	Not identified without deyolking	4.31E+05 ± 4.81E+04
	G3P2_DANRE
G-protein-coupled receptor 98^c,e	F1QEZ1_DANRE	674	0.019	3.56E+03 ± 3.56E+03	2.50E+04 ± 4.30E+03
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1^c,e	GBB1_DANRE	37	0.034	Not identified without deyolking	1.32E+05 ± 4.16E+04
Heat shock 60kD protein 1 (Chaperonin)^c	Q803B0_DANRE	61	0.046	Not identified without deyolking	1.90E+04 ± 6.61E+03
Heterochromatin protein 1, binding protein 3^c	E7FAZ5_DANRE	65	0.017	Not identified without deyolking	6.55E+04 ± 1.65E+04
Heterogeneous nuclear ribonucleoprotein A0, like^c,e	Q7ZU48_DANRE	32a	0.006	Not identified without deyolking	8.92E+04 ± 1.70E+04
Heterogeneous nuclear ribonucleoprotein L^c,e	Q7ZW09_DANRE	59	0.017	Not identified without deyolking	9.16E+04 ± 2.31E+04
Histone H3.2^c	H32_DANRE	15	0.010	6.46E+04 ± 3.93E+04	2.49E+05 ± 9.72E+03
	X1WC76_DANRE
Hydroxysteroid (17-beta) dehydrogenase 10^c	Q5XJS8_DANRE	27	0.017	Not identified without deyolking	4.23E+04 ± 1.07E+04
Malate dehydrogenase^d	Q7T334_DANRE	35	<0.001	3.66E+04 ± 2.70E+04	5.85E+05 ± 8.91E+03
Malic enzyme^c,e	A4QPA0_DANRE	67	0.009	Not identified without deyolking	1.81E+04 ± 3.83E+03
Myosin light chain, phosphorylatable, fast skeletal muscle a^c	O93409_DANRE	19	0.006	2.08E+05 ± 2.71E+04	4.76E+05 ± 4.29E+04
Myosin, heavy polypeptide 1.2, skeletal muscle^f	B8A561_DANRE	222	<0.001	Not identified without deyolking	8.45E+01 ± 4.18E+01^f
NADH dehydrogenase (ubiquinone) alpha subcomplex, 5^c,e	Q5BJA2_DANRE	13	0.003	Not identified without deyolking	4.92E+04 ± 7.63E+03
Nucleoside diphosphate kinase^c,e	Q7SXL4_DANRE	17	0.025	4.41E+04 ± 1.57E+04	1.59E+05 ± 2.92E+04
Periostin, osteoblast specific factor b^c,e	E7FBL9_DANRE	86	0.030	1.01E+04 ± 1.01E+04	5.16E+04 ± 7.47E+03
	F1QHK3_DANRE
	Q75U66_DANRE
Phosphorylase^c,e	Q503C7_DANRE	97	0.034	9.02E+03 ± 9.02E+03	1.64E+05 ± 4.79E+04
Pyrophosphatase (inorganic) 1b^c,e	B7ZD39_DANRE	33	0.015	Not identified without deyolking	9.36E+04 ± 2.29E+04
Pyruvate kinase^d	F1QEN1_DANRE	67a	<0.001	Not identified without deyolking	2.74E+05 ± 8.59E+03
	F1QSE0_DANRE
	F1RBK3_DANRE
Ribosomal protein S5^c,e	Q6PC80_DANRE	23	0.011	Not identified without deyolking	1.76E+05 ± 3.94E+04
Synaptosomal-associated protein 91^c,e	E7F4Z2_DANRE	94	0.049	Not identified without deyolking	5.59E+04 ± 2.00E+04
	E9QBM8_DANRE
Synaptotagmin binding, cytoplasmic RNA interacting protein^c	F1QY96_DANRE	77	0.011	5.81E+04 ± 1.46E+04	2.31E+05 ± 3.56E+04
	Q6NUZ3_DANRE
Titin A^d	F1R7N8_DANRE	3487	0.009	1.86E+04 ± 1.86E+04	1.84E+05 ± 2.95E+04
Titin B^d	F1Q6U3_DANRE	3026	0.026	2.79E+04 ± 2.47E+03	1.60E+05 ± 3.83E+04
Transforming growth factor, beta-induced^c,e	Q503K1_DANRE	74	0.022	Not identified without deyolking	1.03E+05 ± 2.84E+04
Tryosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide^c,e	Q803M8_DANRE	28	<0.001	Not identified without deyolking	1.72E+04 ± 1.35E+03
Tubulin, alpha 1c^f	B8A518_DANRE	50	0.027	2.43E+00 ± 0.72E+00^f	9.96E+00 ± 0.24E+00^f
Ubiquinol-cytochrome c reductase core protein I^c,e	F1QUE3_DANRE	55	0.004	Not identified without deyolking	1.99E+04 ± 3.44E+03
Uncharacterized ionotropic glutamate receptor family protein si:ch211-251b21.1^c	B8JLR6_DANRE	50	<0.001	Not identified without deyolking	1.69E+05 ± 1.43E+04
Uncharacterized actin family protein zgc:86725^d	F1RCB6_DANRE	42	0.001	1.60E+06 ± 7.82E+04	3.27E+06 ± 1.84E+05

Minimum protein identification confidence: 99%, minimum peptide identification confidence: 95% requiring at least 2 peptides per protein. G-test or Student's t-test was accepted at p < 0.05 with at least a 1.5-fold change.

^{^a}

Student's t-test for total MS² TIC, unless significant enrichment was detected only with spectral counting for which the G-test is reported.

^{^b}

Spectral counts, if significant enrichment detected only with spectral counting—otherwise, total MS² TIC. Total MS² TIC and spectral counts are given as average ± standard error.

^{^c}

Significant enrichment detected only using MS² TIC criteria.

^{^d}

Significant enrichment detected with both spectral counting and using MS² TIC criteria.

^{^e}

Identification made by SEQUEST alone.

^{^f}

Significant enrichment detected only with spectral counting.

MS² TIC, MS/MS total ion current.