Table I Histone cross-links with modifications. *identified cross-linked peptide sequence with mass of modifications indicated in brackets following the modified residue. Modifications are: 142.11-mono-methylation, 156.13-di-methylation, 170.11-acetylation, 170.14-tri-methylation, 325.13-BDP stump mass indicating cross-linked residue. ‡ Modification checked against data contained in UniProt for known modification sites. ∧ amino acid residue number for cross-linked site starting with initial Met = 1.
peptide 1*peptide 2*Protein 1 (UniProt)†Protein 2 (UniProt)†peptide 1 modification verification‡peptide 2 modification verification‡pep1 xlink site^pep2 xlink site^
K[142.11]STGGK[325.13]APRTK[325.13]QTARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me, Uniprot144
K[156.13]STGGK[325.13]APRTK[325.13]QTARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me2, Uniprot144
K[142.11]STGGK[325.13]APRK[325.13]QLATKsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me, Uniprot1418
K[156.13]STGGK[325.13]APRK[325.13]QLATKsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me2, Uniprot1418
K[156.13]STGGK[325.13]APRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +2H3K9me2, UniprotH3K23ac, Uniprot1418
K[156.13]SAPATGGVK[325.13]KPHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, Uniprot3656
K[156.13]SAPATGGVK[156.13]K[325.13]PHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me2, Uniprot3756
K[156.13]SAPATGGVK[325.13]KPHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, Uniprot3618
K[142.11]STGGK[325.13]APRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +2H3K9me, UniprotH3K23ac, Uniprot1418
K[156.13]SAPATGGVK[142.11]K[325.13]PHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me, Uniprot3756
K[156.13]SAPATGGVK[325.13]K[142.11]PHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me, Uniprot3656
K[156.13]SAPATGGVK[325.13]KPHRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, UniprotH3K23ac, Uniprot3618
K[156.13]STGGK[325.13]APRYQK[325.13]STELLIRsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me2, Uniprot1456
K[156.13]SAPATGGVK[325.13]KPHRTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, Uniprot364
K[156.13]STGGK[325.13]APRRGGVK[325.13]Rsp P68431 H31_HUMAN +3sp P62805 H4_HUMANH3K9me2, Uniprot1444
K[156.13]SAPATGGVK[156.13]K[325.13]PHRTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me2, Uniprot374
K[156.13]SAPATGGVK[325.13]K[156.13]PHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K37me2, Uniprot3618
K[156.13]SAPATGGVK[142.11]K[325.13]PHRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K36me, UniprotH3K23ac, Uniprot3718
K[156.13]SAPATGGVK[156.13]K[325.13]PHRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K36me2, UniprotH3K23ac, Uniprot3718
K[156.13]SAPATGGVK[325.13]K[156.13]PHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K37me2, Uniprot3656
K[156.13]SAPATGGVK[325.13]KPHRK[325.13]TESHHKsp P68431 H31_HUMAN +2sp P04908 H2A1B_HUMAN +1H3K27me2, Uniprot36119
K[156.13]SAPATGGVK[156.13]K[325.13]PHRK[325.13]TESHHKsp P68431 H31_HUMAN +2sp P04908 H2A1B_HUMAN +1H3K27me2, H3K36me2, Uniprot37119
K[156.13]SAPATGGVK[142.11]K[325.13]PHRK[325.13]TESHHKsp P68431 H31_HUMAN +2sp P04908 H2A1B_HUMAN +1H3K27me2, H3K36me, Uniprot37119
K[156.13]SAPATGGVK[325.13]KPHRK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, UniprotH3K9me2, Uniprot3614
K[142.11]STGGK[325.13]APRK[170.14]SAPATGGVK[325.13]KPHRsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +2H3K9me, UniprotH3K27me3, Uniprot1436
K[142.11]STGGK[325.13]APRK[156.13]SAPATGGVK[325.13]KPHRsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +2H3K9me, UniprotH3K27me2, Uniprot1436
K[156.13]SAPATGGVK[142.11]K[325.13]PHRK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me, UniprotH3K9me2, Uniprot3714
K[156.13]SAPATGGVK[156.13]K[325.13]PHRK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me2, UniprotH3K9me2, Uniprot3714
K[156.13]SAPATGGVK[156.13]K[325.13]PHRK[170.14]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me2, UniprotH3K9me3, Uniprot3714
K[156.13]SAPATGGVK[156.13]K[325.13]PHRRGGVK[325.13]Rsp P68431 H31_HUMAN +2sp P62805 H4_HUMANH3K27me2, H3K36me2, Uniprot3744
K[156.13]SAPATGGVK[156.13]K[325.13]PHRLAHYNK[325.13]Rsp P68431 H31_HUMAN +2sp P33778 H2B1B_HUMAN +2H3K27me2, H3K36me2, Uniprot3785
K[156.13]SAPATGGVK[325.13]K[156.13]PHRTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K37me2, Uniprot364
K[156.13]SAPATGGVK[156.13]K[325.13]PHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me2, Uniprot3718
K[156.13]SAPATGGVK[325.13]KPHRK[325.13]STGGKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, Uniprot369
K[142.11]SAPATGGVK[325.13]KPHRK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me, UniprotH3K9me2, Uniprot3614
K[156.13]SAPATGGVK[325.13]KPHRRGGVK[325.13]Rsp P68431 H31_HUMAN +2sp P62805 H4_HUMANH3K27me2, Uniprot3644
K[156.13]SAPATGGVK[142.11]K[325.13]PHRRGGVK[325.13]Rsp P68431 H31_HUMAN +2sp P62805 H4_HUMANH3K27me2, H3K36me, Uniprot3744
K[156.13]SAPATGGVK[325.13]K[142.11]PHRRGGVK[325.13]Rsp P68431 H31_HUMAN +2sp P62805 H4_HUMANH3K27me2, H3K36me, Uniprot3644
K[156.13]STGGK[325.13]APRK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me2, UniprotH3K9me2, Uniprot1414
K[156.13]SAPATGGVK[142.11]K[325.13]PHRTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me, Uniprot374
K[156.13]SAPATGGVK[142.11]K[325.13]PHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me2, H3K36me, Uniprot3718
K[156.13]SAPSTGGVK[156.13]K[325.13]PHRYQK[325.13]STELLIRsp P84243 H33_HUMANsp P84243 H33_HUMAN +3H3K27me2, H3K36me2, Uniprot3756
K[325.13]STGGK[170.11]APRTK[325.13]QTARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K14ac, Uniprot94
K[325.13]QLATK[170.11]AARTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K14ac, Uniprot184
K[170.14]STGGK[325.13]APRTK[325.13]QTARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me3, Uniprot144
K[170.14]STGGK[325.13]APRK[325.13]QLATKsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K9me3, Uniprot1418
K[170.14]SAPATGGVKK[325.13]PHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me3, Uniprot3756
GLGK[325.13]GGAK[170.11]RLLLPGELAK[325.13]HAVSEGTKsp P62805 H4_HUMANsp P62807 H2B1C_HUMAN +3H4K16ac, Uniprot12108
K[170.14]STGGK[325.13]APRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +2H3K9me3, UniprotH3K23ac, Uniprot1418
K[170.11]SAPATGGVK[325.13]KPHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27ac, Uniprot3656
K[170.14]SAPATGGVK[325.13]KPHRYQK[325.13]STELLIRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me3, Uniprot3656
K[170.14]SAPATGGVK[325.13]KPHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me3, Uniprot3618
K[325.13]QLATK[170.11]AARK[325.13]STGGK[170.11]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K14ac, UniprotH3K14ac, Uniprot189
K[170.14]SAPATGGVK[325.13]KPHRTK[325.13]QTARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me3, Uniprot364
K[170.14]SAPATGGVK[325.13]KPHRK[325.13]QLATK[170.11]AARsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me3, UniprotH3K23ac, Uniprot3618
K[325.13]QLATK[170.11]AARK[325.13]SAPATGGVK[142.11]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K14ac, UniprotH3K36me, Uniprot1827
K[170.14]SAPATGGVK[325.13]KPHRK[325.13]TESHHKsp P68431 H31_HUMAN +2sp P04908 H2A1B_HUMAN +1H3K27me3, Uniprot36119
K[170.14]SAPATGGVK[325.13]KPHRK[170.14]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27me3, UniprotH3K9me3, Uniprot3614
K[170.11]SAPATGGVKK[325.13]PHRK[325.13]QLATKsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K27ac, Uniprot3718
K[325.13]QLATK[170.11]AARK[325.13]SAPATGGVK[156.13]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K14ac, UniprotH3K36me2, Uniprot1827
KQLATK[325.13]AARK[156.13]SAPATGGVK[325.13]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, Uniprot2336
KQLATK[325.13]AARK[142.11]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K9me, Uniprot2314
KQLATK[325.13]AARK[156.13]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K9me2, Uniprot2314
GGK[325.13]GLGKK[156.13]STGGK[325.13]APRsp P62805 H4_HUMANsp P68431 H31_HUMAN +3H3K9me2, Uniprot814
KTESHHK[325.13]AKK[156.13]STGGK[325.13]APRsp P04908 H2A1B_HUMANsp P68431 H31_HUMAN +3H3K9me2, Uniprot12514
GK[325.13]GGKK[156.13]SAPATGGVK[325.13]KPHRsp P62805 H4_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, Uniprot536
KQLATK[325.13]AARK[142.11]SAPATGGVK[325.13]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me, Uniprot2336
KQLATK[325.13]AARK[325.13]SAPATGGVK[142.11]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K36me, Uniprot2327
KQLATK[325.13]AARK[156.13]SAPATGGVK[156.13]K[325.13]PHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K36me2, Uniprot2337
KQLATK[325.13]AARK[156.13]SAPATGGVK[142.11]K[325.13]PHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K36me, Uniprot2337
KQLATK[325.13]AARK[156.13]SAPATGGVK[325.13]K[142.11]PHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K37me, Uniprot2336
KTESHHK[325.13]AKK[156.13]SAPATGGVK[325.13]KPHRsp P04908 H2A1B_HUMANsp P68431 H31_HUMAN +2H3K27me2, Uniprot12536
KQLATK[325.13]AARK[156.13]SAPATGGVK[325.13]K[156.13]PHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me2, H3K37me2, Uniprot2336
GK[325.13]GGKGLGK[325.13]GGAK[170.11]Rsp P62805 H4_HUMAN +2sp P62805 H4_HUMANH4K16ac, Uniprot512
KQLATK[325.13]AARK[170.14]STGGK[325.13]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K9me3, Uniprot2314
KQLATK[325.13]AARK[325.13]STGGK[170.11]APRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +3H3K14ac, Uniprot239
K[325.13]QLATKK[325.13]STGGK[170.11]APRsp P68431 H31_HUMAN +3sp P68431 H31_HUMAN +3H3K14ac, Uniprot189
KQLATK[325.13]AARK[325.13]SAPATGGVK[170.14]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K36me3, Uniprot2327
KQLATK[325.13]AARK[325.13]SAPSTGGVK[170.14]KPHRsp P84243 H33_HUMAN +2sp P84243 H33_HUMANH3K36me3, Uniprot2327
KQLATK[325.13]AARK[170.14]SAPATGGVK[325.13]KPHRsp P68431 H31_HUMAN +2sp P68431 H31_HUMAN +2H3K27me3, Uniprot2336
KTESHHK[325.13]AKK[170.14]STGGK[325.13]APRsp P04908 H2A1B_HUMANsp P68431 H31_HUMAN +3H3K9me3, Uniprot12514