Table I Synthetic peptide sequences and relative quantifications
Peptide numberCST product numberProtein and peptide positionsSynthetic peptide sequence and PTMsMass shift (Da)Endogenous peptide (propionylated) MH+ massSynthetic peptide (propionylated) MH+ massRelative abundance (%)
111188Histone H3 1–8ARTKQTAR8.0141043.5961051.6100.305
211189ARme1TKQTAR8.0141057.6121065.6260.375
311190Histone H3 3–8TKQTAR4.007816.458820.4650.0326
411191TKme1QTAR4.007830.474834.4810.178
511192TKme2QTAR4.007788.463792.4700.0018
611193TKme3QTAR4.007802.478806.4850.0019
711194TphKQTAR4.007896.424900.4310.0055
811195Histone H3 9–17KSTGGKAPR6.0141069.6011075.6140.571
911197Kme1STGGKAPR6.0141083.6161089.6301.295
1011198Kme2STGGKAPR6.0141041.6061047.6190.303
1111199Kme3STGGKAPR12.0211055.6211067.6420.252
1211196KacSTGGKAPR6.0141055.5841061.5980.314
1311200KSTGGKacAPR9.0181055.5841064.6020.378
1411201Kme1STGGKacAPR6.0141069.6001075.6141.014
1511202Kme2STGGKacAPR6.0141027.5891033.6030.177
1611203Kme3STGGKacAPR10.0211041.6051051.6250.156
1711204KacSTGGKacAPR6.0141041.5681047.5820.276
1811205KSphTGGKAPR6.0141149.5661155.5800.238
1911206Kme1SphTGGKAPR6.0141163.5821169.5960.622
2011207Kme2SphTGGKAPR6.0141121.5711127.5850.204
2111208Kme3SphTGGKAPR6.0141135.5871141.6000.160
2211209Histone H3 18–26KQLATKAAR7.0171154.6901161.7071.608
2311211Kme1QLATKAAR7.0171168.7051175.7231.210
2411213KQLATKme1AAR11.0241168.7051179.7301.591
2511210KacQLATKAAR7.0171140.6741147.6911.553
2611212KQLATKacAAR15.0311140.6741155.7051.307
2711214KacQLATKacAAR7.0171126.6571133.6751.711
2811215Histone H3 27–40KSAPATGGVKKPHR6.0141657.9391663.9531.885
2911217Kme1SAPATGGVKKPHR6.0141671.9551677.9682.081
3011218Kme2SAPATGGVKKPHR6.0141629.9441635.9583.201
3111219Kme3SAPATGGVKKPHR10.0211643.9591653.9803.176
3211216KacSAPATGGVKKPHR6.0141643.9231649.9372.305
3311220KSAPATGGVKme1KPHR9.0181671.9551680.9721.870
3411221KSAPATGGVKme2KPHR9.0181629.9441638.9621.678
3511222KSAPATGGVKme3KPHR9.0181643.9591652.9771.762
3611223Kme1SAPATGGVKme1KPHR12.0281685.9701697.9981.377
3711224Kme1SAPATGGVKme2KPHR12.0281643.9591655.9871.377
3811225Kme1SAPATGGVKme3KPHR6.0141657.9751663.9891.670
3911226Kme2SAPATGGVKme1KPHR15.0311643.9591658.9902.288
4011227Kme2SAPATGGVKme2KPHR9.0181601.9491610.9671.619
4111228Kme2SAPATGGVKme3KPHR6.0141615.9641621.9782.119
4211229Kme3SAPATGGVKme1KPHR12.0281657.9751670.0022.840
4311230Kme3SAPATGGVKme2KPHR9.0181615.9641624.9821.653
4411231Kme3SAPATGGVKme3KPHR6.0141629.9791635.9931.746
4511232KSphAPATGGVKKPHR6.0141737.9051743.9191.647
4611233Kme1SphAPATGGVKKPHR6.0141751.9201757.9341.438
4711234Kme2SphAPATGGVKKPHR6.0141709.9101715.9242.894
4811235Kme3SphAPATGGVKKPHR6.0141723.9251729.9392.222
4911242Histone H3 41–49YRPGTVALR7.0171088.6221095.6390.654
5011240Histone H3 54–63YQKSTELLIR7.0171362.7631369.7800.217
5111241YQKacSTELLIR7.0171348.7471355.7640.512
5211236Histone H3 73–83EIAQDFKTDLR7.0171447.7431454.7600.125
5311237EIAQDFKme1TDLR7.0171461.7591468.7760.069
5411238EIAQDFKme2TDLR7.0171419.7481426.7650.548
5511239EIAQDFKme3TDLR7.0171433.7631440.7810.668
5611243Histone H4 1–17acSGRGKGGKGLGKGGAKR7.0171837.0401844.0571.227
5711244acSGRme1GKGGKGLGKGGAKR7.0171851.0561858.0731.878
5811245Histone H4 4–17GKGGKGLGKGGAKR7.0171550.9021557.9191.872
5911246GKGGKGLGKGGAKacR6.0081536.8861542.8931.500
6011247GKGGKGLGKacGGAKR9.0111536.8861545.8971.788
6111248GKGGKacGLGKGGAKR11.0241536.8861547.9101.357
6211249GKacGGKGLGKGGAKR14.0281536.8861550.9141.950
6311250GKacGGKGLGKGGAKacR6.0081522.8691528.8772.011
6411251GKGGKacGLGKGGAKacR7.0171522.8691529.8871.023
6511252GKGGKGLGKacGGAKacR9.0111522.8691531.8811.401
6611253GKacGGKGLGKacGGAKR11.0241522.8691533.8941.431
6711254GKGGKacGLGKacGGAKR13.0251522.8691535.8941.633
6811255GKacGGKacGLGKGGAKR14.0281522.8691536.8971.000
6911256GKGGKacGLGKacGGAKacR6.0081508.8531514.8611.644
7011257GKacGGKGLGKacGGAKacR9.0111508.8531517.8641.317
7111258GKacGGKacGLGKGGAKacR11.0241508.8531519.8771.315
7211259GKacGGKacGLGKacGGAKR14.0281508.8531522.8811.589
7311260GKacGGKacGLGKacGGAKacR7.0171494.8371501.8541.399
7411261Histone H4 20–23KVLR7.017627.419634.4360.946
7511262Kme1VLR7.017641.435648.4521.412
7611263Kme2VLR7.017599.424606.4420.078
7711264Kme3VLR7.017613.440620.4570.075
7811265Histone H4 68–78DAVTYTEHAKR6.0141402.6971408.7100.411
7911274Canonical histone H2A 4–11GKQGGKAR7.011969.548976.5590.329
8011275GKQGGKacAR7.011955.532962.5430.123
8111276GKacQGGKAR10.015955.532965.5460.070
8211277GKacQGGKacAR7.011941.516948.5260.030
8311273Canonical histone H2A 82–88HLQLAIR7.017906.552913.5701.338
8411278Histone H2A.Z 1–19AGGKAGKDSGKAKTKAVSR6.0142153.1932159.2070.720
8511279AGGKacAGKDSGKAKTKAVSR6.0142139.1772145.1900.754
8611280AGGKAGKacDSGKAKTKAVSR9.0182139.1772148.1940.422
8711281AGGKAGKDSGKacAKTKAVSR12.0212139.1772151.1980.616
8811282AGGKAGKacDSGKacAKTKAVSR6.0142125.1602131.1740.338
8911283AGGKacAGKDSGKacAKTKAVSR9.0182125.1602134.1780.944
9011284AGGKacAGKacDSGKAKTKAVSR12.0212125.1602137.1820.756
9111285AGGKacAGKacDSGKacAKTKAVSR6.0142111.1442117.1580.731
9211286Histone macroH2A 44–55SAKAGVIFPVGR6.0141313.7581319.7720.856
9311287Histone H2A.X 4–11GKTGGKAR7.011942.537949.5480.235
  • 93 histone peptides with various PTMs were synthesized with stable isotope (C13 and N15)-labeled amino acids (underlined in the column “Synthetic Peptide Sequence and PTMs”). me1, -2, and -3 denote mono-, di-, and tri-methylation; ph, phosphorylation; ac, acetylation. The peptide number used in Fig. 2 is shown in the first column. Cell Signaling Technology Inc. product numbers are shown in the second column. The averaged relative abundance in the last column represents the detection efficiencies of these peptides.