Table I. Quantification of all valid peptides and PTMs in histone H3 major form.
| WT/15N WT |
TXR1/15N WT |
p valuea | Final ratio |
Normalized |
|||||
|---|---|---|---|---|---|---|---|---|---|
| Mean (S.D.) | Mean (S.D.) | TXR1/WT | TXR1/WT | ||||||
| H3 major | Protein-level ratio |
||||||||
| 1.26 (0.03) | 1.01 (0.19) | 0.13464 | 0.80 | 1.07 | |||||
| Start | End | Sequence | Modificationsb | z | Peptide ratio-level ratios | ||||
| 3 | 8 | TKQTAR | Me1(K4); Pr(N-term) | 2 | 0.74 (0.06) | 0.93 (0.04) | 0.01503 | 1.26 | 1.78 |
| 9 | 17 | KSTGAKAPR | Pr(N-term, K14) | 2 | 0.94 (0.04) | 0.68 (0.09) | 0.022982 | 0.73 | 1.02 |
| 9 | 17 | KSTGAKAPR | Pr(N-term, K9, K14) | 1 | 0.82 (0.04) | 0.53 (0.05) | 0.002279 | 0.65 | 0.91 |
| 9 | 17 | KSTGAKAPR | Ac(K14); Pr(N-term) | 2 | 1.40 (0.35) | 1.25 (0.11) | 0.538428 | 0.89 | 1.24 |
| 18 | 26 | KQLASKAAR | Ac(K18, K23); Pr(N-term) | 1 | 1.19 (0.08) | 1.17 (0.13) | 0.816231 | 0.98 | 1.36 |
| 2 | 1.15 (0.04) | 1.16 (0.12) | 0.872236 | 1.01 | 1.41 | ||||
| 18 | 26 | KQLASKAAR | Ac(K23); Pr(N-term, K18) | 1 | 0.98 (0.04) | 0.90 (0.11) | 0.322315 | 0.91 | 1.27 |
| 2 | 0.99 (0.03) | 0.96 (0.11) | 0.685553 | 0.97 | 1.35 | ||||
| 18 | 26 | KQLASKAAR | Ac(K18); Pr(N-term, K23) | 2 | 0.99 (0.03) | 0.96 (0.10) | 0.669132 | 0.97 | 1.35 |
| 18 | 26 | KQLASKAAR | Me1(K23); Pr(N-term, K18, K23) | 2 | 0.63 (0.17) | 1.13 (0.09) | 0.019933 | 1.79 | 2.52 |
| 18 | 26 | KQLASKAAR | Pr(N-term, K18, K23) | 1 | 1.18 (0.05) | 0.87 (0.10) | 0.016895 | 0.74 | 1.02 |
| 2 | 1.20 (0.05) | 0.96 (0.17) | 0.126337 | 0.80 | 1.12 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Pr(N-term, K36, K37) | 2 | 2.16 (0.40) | 5.25 (1.03) | 0.023132 | 2.43 | 3.34 |
| 3 | 2.18 (0.48) | 5.20 (0.98) | 0.018246 | 2.39 | 3.29 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Me1(K27); Pr(N-term, K36, K37) | 2 | 1.36 (0.05) | 0.25 (0.03) | 8.29 × 10−5 | 0.19 | 0.26 |
| 3 | 1.30 (0.04) | 0.27 (0.03) | 1.47 × 10−5 | 0.21 | 0.29 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Me2(K27); Pr(N-term, K36, K37) | 2 | 0.98 (0.08) | 0.40 (0.05) | 0.000824 | 0.41 | 0.56 |
| 3 | 0.87 (0.03) | 0.34 (0.04) | 0.000115 | 0.40 | 0.55 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Me3(K27); Pr(N-term, K36, K37) | 2 | 0.63 (0.03) | 0.44 (0.04) | 0.040226 | 0.70 | 0.92 |
| 3 | 0.61 (0.04) | 0.38 (0.05) | 0.005474 | 0.63 | 0.91 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Me1(K27, K36); Pr(N-term, K36, K37) | 2 | 0.59 (0.22) | 0.05 (0.02) | 0.049941 | 0.09 | 0.13 |
| 3 | 0.74 (0.08) | 0.06 (0.00) | 0.004257 | 0.08 | 0.11 | ||||
| 27 | 40 | KSAPATGGIKKPHR | Ac(K27); Pr(N-term, K36, K37) | 2 | 0.99 (0.10) | 1.06 (0.09) | 0.37916 | 1.08 | 1.50 |
| 27 | 40 | KSAPATGGIKKPHR | Me1(K27); Pr(N-term, K27, K36, K37) | 2 | 1.35 (0.04) | 0.18 (0.02) | 4.17 × 10−5 | 0.13 | 0.18 |
| 27 | 40 | KSAPATGGIKKPHR | Pr(N-term, K27, K36, K37) | 2 | 2.19 (0.43) | 4.98 (0.92) | 0.020405 | 2.27 | 3.12 |
| 27 | 40 | KSAPATGGIKKPHR | Me1(K36); Pr(N-term, K27, K36, K37) | 2 | 1.30 (0.09) | 0.15 (0.01) | 0.001829 | 0.12 | 0.16 |
| 27 | 40 | KSAPATGGIKKPHR | Me1(K27, K36); Pr(N-term, K27, K36, K37) | 2 | 0.79 (0.10) | 0.06 (0.00) | 0.005714 | 0.08 | 0.11 |
| 27 | 40 | KSAPATGGIKKPHR | Me1(K36); Me2(K27); Pr(N-term, K36, K37) | 3 | 0.58 (0.08) | 0.37 (0.02) | 0.160328 | 0.64 | 1.02 |
| 28 | 40 | SAPATGGIKKPHR | Pr(N-term, K36, K37) | 2 | 4.92 (0.82) | 4.98 (2.56) | 0.978241 | 1.01 | 1.24 |
| 41 | 49 | FRPGTVALR | Pr(N-term) | 2 | 1.31 (0.15) | 1.01 (0.17) | 0.087001 | 0.77 | 1.07 |
| 53 | 63 | KYQKSTDLLIR | Pr(N-term, K56) | 2 | 1.24 (0.12) | 1.00 (0.15) | 0.093877 | 0.80 | 1.11 |
| 53 | 63 | KYQKSTDLLIR | Me1(K56); Pr(N-term, K56) | 2 | 0.66 (0.14) | 1.17 (0.04) | 0.019107 | 1.77 | 2.49 |
| 54 | 63 | YQKSTDLLIR | Pr(N-term) | 1 | 1.13 (0.01) | 0.87 (0.01) | 0.394434 | 0.77 | 0.90 |
| 2 | 1.38 (0.21) | 1.01 (0.40) | 0.001585 | 0.73 | 1.23 | ||||
| 70 | 83 | LVRDIAHEFKAELR | Pr(N-term, K79) | 2 | 1.06 (0.19) | 1.02 (0.16) | 0.825064 | 0.96 | 1.34 |
| 73 | 83 | DIAHEFKAELR | Pr(N-term, K79) | 1 | 1.26 (0.24) | 1.04 (0.24) | 0.569269 | 0.83 | 1.26 |
| 2 | 1.13 (0.24) | 1.03 (0.15) | 0.461435 | 0.91 | 1.06 | ||||
| 73 | 83 | DIAHEFKAELR | Me1(R83); Pr(N-term, K79) | 2 | 1.16 (0.03) | 1.06 (0.25) | 0.675039 | 0.92 | 1.17 |
| 116 | 128 | RVTIMTKDMQLAR | Pr(N-term, K122) | 2 | 0.99 (0.30) | 0.99 (0.12) | 0.746262 | 1.00 | 1.30 |
| 3 | 1.00 (0.35) | 0.92 (0.12) | 0.982936 | 0.92 | 1.39 | ||||
| 117 | 128 | VTIMTKDMQLAR | Pr(N-term, K122) | 1 | 1.05 (0.25) | 1.10 (0.19) | 0.808235 | 1.05 | 1.45 |
| 2 | 1.07 (0.24) | 1.06 (0.17) | 0.959774 | 0.99 | 1.37 | ||||
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.