Table I Quantification of all valid peptides and PTMs in histone H3 major form
WT/15N WTTXR1/15N WTp valueaFinal ratioNormalized
Mean (S.D.)Mean (S.D.)TXR1/WTTXR1/WT
H3 majorProtein-level ratio
1.26 (0.03)1.01 (0.19)0.134640.801.07
StartEndSequenceModificationsbzPeptide ratio-level ratios
38TKQTARMe1(K4); Pr(N-term)20.74 (0.06)0.93 (0.04)0.015031.261.78
917KSTGAKAPRPr(N-term, K14)20.94 (0.04)0.68 (0.09)0.0229820.731.02
917KSTGAKAPRPr(N-term, K9, K14)10.82 (0.04)0.53 (0.05)0.0022790.650.91
917KSTGAKAPRAc(K14); Pr(N-term)21.40 (0.35)1.25 (0.11)0.5384280.891.24
1826KQLASKAARAc(K18, K23); Pr(N-term)11.19 (0.08)1.17 (0.13)0.8162310.981.36
21.15 (0.04)1.16 (0.12)0.8722361.011.41
1826KQLASKAARAc(K23); Pr(N-term, K18)10.98 (0.04)0.90 (0.11)0.3223150.911.27
20.99 (0.03)0.96 (0.11)0.6855530.971.35
1826KQLASKAARAc(K18); Pr(N-term, K23)20.99 (0.03)0.96 (0.10)0.6691320.971.35
1826KQLASKAARMe1(K23); Pr(N-term, K18, K23)20.63 (0.17)1.13 (0.09)0.0199331.792.52
1826KQLASKAARPr(N-term, K18, K23)11.18 (0.05)0.87 (0.10)0.0168950.741.02
21.20 (0.05)0.96 (0.17)0.1263370.801.12
2740KSAPATGGIKKPHRPr(N-term, K36, K37)22.16 (0.40)5.25 (1.03)0.0231322.433.34
32.18 (0.48)5.20 (0.98)0.0182462.393.29
2740KSAPATGGIKKPHRMe1(K27); Pr(N-term, K36, K37)21.36 (0.05)0.25 (0.03)8.29 × 10−50.190.26
31.30 (0.04)0.27 (0.03)1.47 × 10−50.210.29
2740KSAPATGGIKKPHRMe2(K27); Pr(N-term, K36, K37)20.98 (0.08)0.40 (0.05)0.0008240.410.56
30.87 (0.03)0.34 (0.04)0.0001150.400.55
2740KSAPATGGIKKPHRMe3(K27); Pr(N-term, K36, K37)20.63 (0.03)0.44 (0.04)0.0402260.700.92
30.61 (0.04)0.38 (0.05)0.0054740.630.91
2740KSAPATGGIKKPHRMe1(K27, K36); Pr(N-term, K36, K37)20.59 (0.22)0.05 (0.02)0.0499410.090.13
30.74 (0.08)0.06 (0.00)0.0042570.080.11
2740KSAPATGGIKKPHRAc(K27); Pr(N-term, K36, K37)20.99 (0.10)1.06 (0.09)0.379161.081.50
2740KSAPATGGIKKPHRMe1(K27); Pr(N-term, K27, K36, K37)21.35 (0.04)0.18 (0.02)4.17 × 10−50.130.18
2740KSAPATGGIKKPHRPr(N-term, K27, K36, K37)22.19 (0.43)4.98 (0.92)0.0204052.273.12
2740KSAPATGGIKKPHRMe1(K36); Pr(N-term, K27, K36, K37)21.30 (0.09)0.15 (0.01)0.0018290.120.16
2740KSAPATGGIKKPHRMe1(K27, K36); Pr(N-term, K27, K36, K37)20.79 (0.10)0.06 (0.00)0.0057140.080.11
2740KSAPATGGIKKPHRMe1(K36); Me2(K27); Pr(N-term, K36, K37)30.58 (0.08)0.37 (0.02)0.1603280.641.02
2840SAPATGGIKKPHRPr(N-term, K36, K37)24.92 (0.82)4.98 (2.56)0.9782411.011.24
4149FRPGTVALRPr(N-term)21.31 (0.15)1.01 (0.17)0.0870010.771.07
5363KYQKSTDLLIRPr(N-term, K56)21.24 (0.12)1.00 (0.15)0.0938770.801.11
5363KYQKSTDLLIRMe1(K56); Pr(N-term, K56)20.66 (0.14)1.17 (0.04)0.0191071.772.49
5463YQKSTDLLIRPr(N-term)11.13 (0.01)0.87 (0.01)0.3944340.770.90
21.38 (0.21)1.01 (0.40)0.0015850.731.23
7083LVRDIAHEFKAELRPr(N-term, K79)21.06 (0.19)1.02 (0.16)0.8250640.961.34
7383DIAHEFKAELRPr(N-term, K79)11.26 (0.24)1.04 (0.24)0.5692690.831.26
21.13 (0.24)1.03 (0.15)0.4614350.911.06
7383DIAHEFKAELRMe1(R83); Pr(N-term, K79)21.16 (0.03)1.06 (0.25)0.6750390.921.17
116128RVTIMTKDMQLARPr(N-term, K122)20.99 (0.30)0.99 (0.12)0.7462621.001.30
31.00 (0.35)0.92 (0.12)0.9829360.921.39
117128VTIMTKDMQLARPr(N-term, K122)11.05 (0.25)1.10 (0.19)0.8082351.051.45
21.07 (0.24)1.06 (0.17)0.9597740.991.37
  • a Species with significant p values (p < 0.05) are boxed. The p value is calculated from peptides that are present at least twice in replicate wild-type (WT) or knockout cells. The average coefficients of variation for peptides from histone H3 in WT and TXR1 knockout cells are 12.7% and 14.2%, respectively.

  • b PTM abbreviations: Ac, acetylation; Me, monomethylation; Me2, dimethylation; Me3, trimethylation; Pr, propionylation.