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

Table 2.

Significantly Depleted 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
AHNAK nucleoprotein^c,d	F1QZ50_DANRE	685	0.001	1.40E+05 ± 1.33E+04	4.03E+03 ± 4.03E+03
	F1R1J9_DANRE
Apolipoprotein A-II^e	B3DFP9_DANRE	16a	0.026	7.27E+00 ± 2.57E+00^b	1.16E+00 ± 0.16E+00^b
Apolipoprotein Bb, tandem duplicate 1^f	F1QQ87_DANRE	413	0.002	5.00E+05 ± 5.90E+04	8.77E+04 ± 9.96E+03
	Q5TZ29_DANRE
ATPase, Ca⁺⁺ transporting, cardiac muscle, fast twitch 1^f	Q5U3A4_DANRE	110	0.008	9.65E+05 ± 1.33E+05	2.60E+05 ± 5.70E+04
	Q642Z0_DANRE
Crystallin, gamma M2d17^d	A6H8Q4_DANRE	21	0.008	1.29E+05 ± 8.07E+03	5.17E+04 ± 1.37E+04
	B0S6N1_DANRE
Keratin 4^f	F1QK60_DANRE	54	0.002	1.69E+06 ± 2.28E+05	8.20E+04 ± 5.21E+04
Keratin type 1 c19e^d	Q1LXJ9_DANRE	50	0.049	1.27E+05 ± 4.56E+04	Completely removed by deyolking
Myosin, heavy chain b^c,f	F1QVX3_DANRE	223	0.041	1.70E+06 ± 1.27E+05	6.43E+05 ± 3.32E+05
	X1WF87_DANRE
Myosin, heavy polypeptide 1.1, skeletal muscle^c,f	B8A568_DANRE	222	0.013	7.03E+06 ± 2.77E+05	5.62E+06 ± 1.83E+05
Myosin, heavy polypeptide 1.3, skeletal muscle^c,d	B8A569_DANRE	222	0.009	6.94E+06 ± 3.11E+05	5.29E+06 ± 1.45E+05
Myosin, heavy polypeptide 2, fast muscle specific^d	Q6IQX1_DANRE	222	0.013	5.25E+06 ± 1.32E+05	4.45E+06 ± 1.35E+05
Type I cytokeratin, enveloping layer, like^c,f	E7FCX7_DANRE	46	0.028	2.02E+05 ± 5.99E+04	Completely removed by deyolking
	E9QDY3_DANRE
	Q1LXJ7_DANRE
	Q9PWD8_DANRE
Uncharacterized histone 2 family protein si:ch211-113a14.11^f	R4GE02_DANRE	27	0.036	7.40E+06 ± 5.81E+05	5.24E+06 ± 3.86E+05
Vitellogenin 1^f	Q1LWN2_DANRE	149	<0.001	1.77E+06 ± 6.66E+04	1.35E+04 ± 6.93E+03
Vitellogenin 2^f	Q1MTC4_DANRE	180	<0.001	7.11E+05 ± 2.14E+04	Completely removed by deyolking
Vitellogenin 5^f	F1R2S5_DANRE	149	<0.001	1.18E+06 ± 7.16E+04	Completely removed by deyolking
Vitellogenin 7^f	F1R2T3_DANRE	149	0.002	1.64E+06 ± 2.12E+05	7.65E+03 ± 7.65E+03
	Q1MTC6_DANRE

Minimum protein identification confidence: 99%, minimum peptide identification confidence: 95% requiring at least two 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}

Identification made by SEQUEST alone.

^{^d}

Significant enrichment detected only using MS² TIC criteria.

^{^e}

Significant enrichment detected only with spectral counting.

^{^f}

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