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. Author manuscript; available in PMC: 2011 Mar 15.
Published in final edited form as: Mol Biosyst. 2010 Aug 6;6(10):2004–2014. doi: 10.1039/c005242f

Table 1.

The complete list of heavy isotope labeled peptides that were synthesized to detect and quantify yeast and human poly-Ub chains and the linkages they contain. Linear, branched (K-GG) and phosphorylated peptides were synthesized to cover Ub and poly-Ub chain as well as their post translationally modified forms. The five most intense transitions (Q1/Q3) for each peptide (except for peptide IQDK) in heavy and light form, respectively, are listed for a complete assay. The bold letters in the sequence of peptides (# 4–11) show sequence variability between human and yeast ubiquitin. Signal intensities of the specific transitions were normalized to the most intense signal set to 100%.

# Sequence Location Modification Organism Q1(H)_Q1(L) Q3(H)_Q3(L) Relative
intensity (%)		 CE
1 MQIFVK 1_6 — Yeast 387.2_383.2 260.1_260.1 100 23
Human 387.2_383.2 514.3_506.3 91 23
387.2_383.2 642.4_634.4 49 23
387.2_383.2 254.2_246.2 45 30
387.2_383.2 520.3_520.3 4 23
2 MQIFV[K_GG]TLTGK 1_11 Branched Yeast 463.3_460.6 313.2_305.2 100 27
Human 463.3_460.6 527.3_519.3 72 24
463.3_460.6 385.2_381.2 56 22
463.3_460.6 373.2_373.2 46 27
463.3_460.6 564.8_560.8 38 22
3 TLTGK 7_11 — Yeast 264.2_260.2 313.2_305.2 100 17
Human 264.2_260.2 426.3_418.3 12 17
176.4_173.8 212.1_204.1 4 17
264.2_260.2 373.2_373.2 1 17
264.2_260.2 316.2316.2 1 17
4 TLTG[K_GG]TITLEVESSDTIDNVK 7_27 Branched Yeast 796.1_793.4 986.5_978.5 100 40
796.1_793.4 1115.5_1107.5 84 40
796.1_793.4 899.5_891.4 61 40
796.1_793.4 1214.6_1206.6 52 39
796.1_793.4 697.4_689.4 52 42
5 TLTG[K_GG]TITLEVEPSDTIENVK 7_27 Branched Human 804.1_801.4 1010.5_1002.5 100 38
804.1_801.4 1139.6_1131.6 18 38
804.1 801.4 1098.5_1094.6 13 30
804.1_801.4 913.5_905.5 12 46
804.1_801.4 1172.6_1172.7 12 38
6 TITLEVESSDTIDNVKSK 12_29 — Yeast 663_660.3 887_882.9 100 27
663_660.3 779.9_775.9 17 27
663_660.3 836.4_832.4 16 27
663_660.3 1330.7_1322.6 12 34
663_660.3 1201.6_1193.6 11 34
7 TITLEVEPSDTIENVK 12_27 — Human 599.3_596.6 505.8_501.8 100 27
898.5_894.5 1010.5_1002.5 84 41
898.5_894.5 1139.6_1131.6 39 41
898.5_894.5 1238.6_1230.6 27 41
599.3_596.6 497.3_489.3 23 27
8 TITLEVESSDTIDNV[K_GG]SK 12_29 Branched Yeast 701_698.4 944_940 100 29
701_698.4 812.4_804.41 28 36
701_698.4 315.7_1307.6 21 36
701_698.4 893.5_889.4 14 29
701_698.4 836.9_832.9 8 29
9 TITLEVEPSDTIENV[K_GG]AK 12_29 Branched Human 703.7_701 948_944 100 28
703.7_701 1323.7_1315.7 59 32
703.7_701 810.5_802.4 51 36
703.7_701 840.9_836.9 31 32
703.7_701 776.4_772.4 20 32
10 S[K_GG]IQDK 28_33 Branched Yeast 420.7_416.7 511.3_503.3 100 25
280.8_278.2 398.2_390.2 65 16
280.8_278.2 330.2_330.2 59 12
280.8_278.2 511.3_503.3 51 16
420.7_416.7 270.2_262.1 33 25
11 A[K_GG]IQDK 28_33 Branched Human 412.7_408.7 511.3_503.3 100 28
275.5_272.8 398.2_390.2 53 15
412.8_408.7 270.2_262.1 39 32
275.5_272.8 511.3_503.3 34 15
275.5_272.8 314.2_314.2 28 15
12 IQDK 30_33 — Yeast 256.2_252.1 398.2_390.2 100 15
Human 171.1_168.4 270.2_262.1 13 13
256.2_252.1 357.2_357.2 4 16
171.1_168.4 242.2_242.2 3 12
13 IQD[K_GG]EGIPPDQQR 30_42 Branched Yeast 549.9_546.6 653.3_643.3 100 36
Human 549.9_546.6 750.4_740.4 100 29
549.9_546.6 441.2_431.2 78 43
549.9_546.6 498.3_493.3 19 22
549.9_546.6 785.4_785.4 13 29
14 EGIPPDQQR 34_43 — Yeast 525.3_520.3 750.4_740.4 100 29
Human 525.3_520.3 653.3_643.3 52 30
350.5_347.2 375.7_370.7 37 17
525.3_520.3 441.2_431.2 30 31
525.3_520.3 556.3_546.3 7 31
15 LIFAGK 43_48 — Yeast 328.7_324.7 430.3_422.2 100 20
Human 328.7_324.7 543.3_535.3 29 20
219.5_216.8 283.2_275.2 12 12
328.7_324.7 272.2_268.2 3 20
328.7_324.7 374.2_374.2 2 20
16 LIFAG[K_GG]QLEDGR 43_54 Branched Yeast 490.9_487.6 622.8_617.8 100 19
Human 490.9_487.6 357.2_347.2 26 33
490.9_487.6 599.3_589.3 24 33
490.9_487.6 549.3_544.3 19 26
490.9_487.6 727.4_717.4 16 33
17 QLEDGR 49_54 — Yeast 364.2_359.2 486.2_476.2 100 25
Human 364.2_359.2 486.2_486.2 100 25
364.2_359.2 599.3_589.3 13 25
364.2_359.2 300.2_295.2 5 21
364.2_359.2 543.2_543.2 2 26
18 TLSDYNIQK 55_63 — Yeast 545.3_541.3 875.4_867.4 100 29
Human 545.3_541.3 673.4_665.4 20 31
545.3_541.3 396.3_388.3 12 32
545.3_541.3 788.4_780.4 9 30
545.3_541.3 494.8_490.8 5 30
19 TL[S_Phos]DYNIQK 55_63 Phosphorylated Yeast 585.3_581.3 955.4_947.4 100 24
Human 585.3_581.3 510.3_502.3 30 31
585.3_581.3 673.4_665.4 28 38
585.3_581.3 534.7_530.7 14 31
585.3_581.3 788.4_780.4 13 31
20 TLSDYNIQ[K_GG]ESTLHLVLR 55_72 Branched Yeast 752.1_748.7 1020.5_1015.5 100 32
Human 752.1_748.7 1077.6_1067.6 24 46
752.1_748.7 647.4_637.4 21 46
752.1_748.7 1319.81309.8 13 46
752.1_748.7 948.6_938.6 12 46
21 TLSDYNIQ[K_GG]E[S_Phos]TLHLVLR 55_72 Branched Yeast 778.7_775.4 1060.51055.5 100 37
Phosphorylated Human 778.7_775.4 647.4_637.4 45 43
778.7_775.4 10171012 33 33
778.7_775.4 959.5_954.5 31 37
778.7_775.4 700.4_695.4 9 37
22 TL[S_Phos]DYNIQ[K_GG]ESTLHLVLR 55_72 Branched Yeast 778.7_775.4 1060.51055.5 100 37
Phosphorylated Human 778.7_775.4 1077.6_1067.6 53 43
778.7_775.4 647.4_637.4 45 43
778.7_775.4 948.6_938.6 44 43
778.7_775.4 838_833 36 38
23 ESTLHLVLR 64_72 — Yeast 359.9_356.5 431.2_431.2 100 17
Human 359.9_356.5 298.2_288.2 78 18
359.9_356.5 431.3_426.3 77 17
359.9_356.5 510.4_500.4 60 23
359.9_356.5 397.3_387.3 43 23
24 E[S_Phos]TLHLVLR 64_72 Phosphorylated Yeast 579.3_574.3 510.4_500.4 100 38
Human 386.5_383.2 510.4_500.4 83 27
579.3_574.3 647.4_637.4 76 38
386.5_383.2 324.2_319.2 51 27
386.5_383.2 324.6_324.6 50 27