(E)IEDGQDGGVpTPYSNE(S) Pol II RPB 1 Figure 5a in article V8 LTQ (CID) Mascot Score: 6 73_sm15_8 #734 RT: 42.82 AV: 1 NL: 1.7E4 T: ITMS + c NSI d w Full ms2 831.8@cid35. [215.-.] 79.22 871.34 dance Relative Abun 45 35 25 15 5 782.14 773.14 69. 954.34 1312.38 1118.27 658. 592.37 1381.35 349. 1294.35 1399.51 525.22 1513.39 6 8
(E)IEDGQDGGVpTPYSNE(S) Pol II RPB 1 Figure 5b in article V8 LTQ (ETD) Mascot Score: 79 73_sm15_8 #71 RT: 43.34 AV: 1 NL: 1.13E4 T: ITMS + c NSI d sa Full ms2 8.82@etd1. [.-.] 8.84 15.45 Relative Abunda ance 6. 5.5 5. 4.5 4. 3.5 3. 2.5 2. 1.5 1..5. 374.43 455.46 559.74 675.27 615.16 732.32 887.33 954.28 13.29 1165. 1287.33 1328.22 1416.6 6 8 1486.
(Y)MPEQKITEIEDGQDGGVpTPY(S) Pol II RPB 1 Chymotrypsin LTQ FT (CID) Mascot Score: 1 74_sm15_9 #75 RT: 64. AV: 1 NL: 2.3E4 T: ITMS + c NSI d w Full ms2 1145.@cid35. [5.-.] 95.72 nce Relative Abunda 45 35 25 15 5 956.15 1314. 1217.23 1615.65 673.21 1827.68 875.36 575.38 1499.55 19.69 461.19 1459.35 1671.99 6 8 16 18
(Y)MPEQKITEIEDGQDGGVpTPY(S) Pol II RPB 1 Chymotrypsin LTQ (ETD) Mascot Score: 96 73_sm15_ #9853 RT: 56.86 AV: 1 NL: 9.98E4 T: ITMS + c NSI d sa Full ms2 1144.26@etd1. [.-.] 1144.31 dance Relative Abun 6 6. 5.5 5. 4.5 4. 35 3.5 3. 2.5 2. 1.5 1..5. 744.53 6.52 845.7 958.56 72.76 1314.44 13.55 1515.46 1687.65 1913.82 1785.48 1631.6565 1929.67 6 8 16 18
(E)LIAEEpSEDDSE(S) Pol II RPB 2 V8 LTQ FT (CID) Mascot Score: 49 74_sm15_13 #3143 RT: 39.95 AV: 1 NL: 9.7E2 T: ITMS + c NSI d w Full ms2 658.74@cid35. [17.-13.] 69.89 1169.23 45 nce Relative Abunda 35 25 15 5 556.18 743.5 761.7 852.14 82.25 622.72 872.2222 967.28 1151.31 465. 235.17 694.56 19. 298.22 822.85 527.38 418.75 898.67 6 7 8 9 1
(R)IRGNLMGKRVDFpSARpTVISGDPNLELDQVGVPK(S) Pol II RPB 3 Trypsin LTQ (CID) Mascot Score: 81 73_sm15_4b #8 RT: 62.13 AV: 1 NL: 1.79E5 T: ITMS + c NSI d w Full ms2 9.94@cid35. [245.-.] 18.61 9 8 Relative Abunda nce 7 6 373.19.24 841. 784.54 984.56 742.43 573.28 97.53 1423.67 1481.68 1567.74 1637.64 6 8 16 18 1681.67 y3 y16 eliminates other possibilities
(R)IRGNLMGKRVDFpSARpTVISGDPNLELDQVGVPK(S) Pol II RPB 3 Trypsin LTQ (ETD) same precursor as CID fragmented (previous slide) Mascot Score: 67 73_sm15_4b #9 RT: 62.13 AV: 1 NL: 1.89E5 T: ITMS + c NSI d sa Full ms2 9.94@etd1. [.-.] 941.26 1864.92 12 nce Relative Abunda 11 9 8 7 6 5 4 3 2 1 969. 1836.82 18.41 1751.72 18.68 82.58 1554.37 612.38 1497.57 727.51 839.81 127.53 1664.56 384.9 583.97 6 8 16 18 z4 z16 eliminates other possibilities
(R)EASKDNVDFILp(SNVDLAMANS)LRR(V) Pol II RPB 3 Trypsin LTQ (CID) Mascot Score: 48 73_sm15_4b #12563 RT: 77.46 AV: 1 NL: 8.84E3 T: ITMS + c NSI d w Full ms2 925.66@cid35. [2.-.] 1119.43 Relative Abunda nce 9 8 7 6 329.24 529.12 642.41 731.44 881.31 824.54 11.42 89.87 988. 1232.53 1319.59 495. 1533.76 1398.55 6 8 16 1687.72 b13, b14, b15 eliminate all other serines ETD spectra confirms was also next scan
(R)EASKDNVDFILSNVDLAMANpSLRR(V) Pol II RPB 3 Trypsin LTQ (ETD) Mascot Score: 53 73_sm15_4b #12564 RT: 77.46 AV: 1 NL: 1.E4 T: ITMS + c NSI d sa Full ms2 925.66@etd1. [.-.] 925.69 24 nce 22 18 16 14 12 1387.91 1833.83 8 185.75 875. 1777.76 6 1335.44 4 1248.37 1548.75 76.15 2 957.68 14.74 1135.45 339.24 435.46 549. 198.45 6 8 16 18 Relative Abunda16 c14, c15, c16 eliminate all other serines CID spectra confirms preceeding scan
(E)DFDVEHFpSDEE(T) Pol II RPB 6 V8 LTQ FT (CID) Mascot Score: 69 74_sm15_13 #6917 RT: 77.7 AV: 1 NL: 1.49E4 T: ITMS + c NSI d w Full ms2 724.75@cid35. [185.-146.] 675.92 24 nce 22 18 16 14 12 8 Relative Abunda16 6 4 2 62.49 691. 89.21 972.26 88.34 262.95 378.14 874.39 477. 593.53 277.23 13.34 11.33 1337.25 6 8
(E)DFDVEHFpSDEE(T) Pol II RPB 6 V8 LTQ (ETD) Mascot Score: 44 73_sm15_12 #11311 RT: 69.13 AV: 1 NL: 9.88E3 T: ITMS + c NSI d sa Full ms2 725.98@etd1. [.-.] 724.65 nce Relative Abunda 45 35 25 1318. 1448.62 1432.36 15 96.2 1171.1313 73.5 1274.13 828.21 957.31 148.29 5 1.57 715.71 269.13 15.78 6 8
(K)SEGpSGSSLVQK(G) Pol III RPC 4 Trypsin LTQ FT (CID) Mascot Score: 58 74_sm15_3 #1724 RT: 28.18 AV: 1 NL: 1.47E3 T: ITMS + c NSI d w Full ms2 579.76@cid35. [145.-117.] 5.94 24 422.91 22 521.77 844.36 942.32 nce 18 16 14 12 8 6 4 2 Relative Abunda16 217.9 275.27 374.35 3.98 487.38 343.19 661.35 544.8 654.17 718.49 786.28 914.35 12.36 7.45 6 7 8 9 1
(K)SEGpSGSSLVQK(G) Pol III RPC 4 Trypsin LTQ (ETD) Mascot Score: 55 73_sm15_6 #494 RT: 29.28 AV: 1 NL: 7.27E3 T: ITMS + c NSI d sa Full ms2 58.3@etd1. [.-.] 579.75 29.33 1142.36 dance Relative Abun 24 22 18 16 14 12 8 6 472.36 559.36 646.36 72.24 55.31 1158.47 4 869. 2 81.23 926.31 255.23 413. 527.57 986.17 6 7 8 9 1
(R)NLIEDEDDGEpSEK(S) Pol III RPC 4 Trypsin LTQ FT (CID) Mascot Score: 51 74_sm15_3 #3489 RT: 43.28 AV: 1 NL: 7.38E2 T: ITMS + c NSI d w Full ms2 786.81@cid35. [5.-1585.] 9 8 737.79 13.25 1214.25 1345.34 1232.27 Relative Abunda nce 7 6 341.31 443.15 673.42 685.48 859.15 97. 944.28 5.36 323.34 585.33 755.64 1426.27 568.31 1459.37 6 8
(R)EIQEALpSEKPTR(E) Pol III RPC 4 Trypsin LTQ (ETD) Mascot Score: 62 73_sm15_6 #5454 RT: 33.1 AV: 1 NL: 1.14E4 T: ITMS + c NSI d sa Full ms2 494.54@etd1. [.-.] 733.8 9 1465.63 8 Relative Abunda nce 7 6 175.13 26.12 494.47 517.21 718.93 741.53 1323.46 997.31 1437.61 965.32 71.35 781.28 94.37 388.23 1222.49 614.34 868.27 1513.91 6 8
(K)KNIKKKDpTKDALSTRELAGK(V) Pol III RPC 4 Lys C LTQ (ETD) Mascot Score: 47 73_sm15_18 #5556 RT: 33.16 AV: 1 NL: 1.51E4 T: ITMS + c NSI d sa Full ms2 387.83@etd1. [.-19.] 1145.54 Relative Abunda nce 9 8 7 6 387.37 581.12 661.42 572.68 1.12 93.53 79.48 31.56 259.18 372.2 12.52 846.55 116.73 479.92 758.28 959.48 4. 317.11 188.11 688.38 147.15 z2 z9 suggests T8 6 8
(K)RSGpSNAAASLPSK(K) Pol III RPC 3 Lys C LTQ (ETD) Mascot Score: 81 73_sm15_18 #4589 RT: 25.99 AV: 1 NL: 2.74E3 T: ITMS + c NSI d sa Full ms2 442.74@etd1. [.-1785.] 13.68 9 8 Relative Abunda nce 7 6 655.46 899.37 812.39 599.24 663.41 1327.62 1196.47 428.19 741.32 515.32 1153.44 174.22 25.49 1293.59 318.24 158.9 956.42 6 8
(E)VKAEDDpTGEEEE(D) Pol III RPC 37 V8 LTQ FT (CID) Mascot Score: 51 74_sm15_15 #1113 RT: 23.91 AV: 1 NL: 7.78E2 T: ITMS + c NSI d w Full ms2 715.77@cid35. [185.-1445.] 667.8 593. 1154.33 25.28 45 nce Relative Abunda 35 25 15 5 259.13 277.12 428.36 477.3 584.43 543.32 675.25 888. 56.37 13.26 839.27 1283.34 1331.35 6 8
(E)VKAEDDpTGEEEE(D) Pol III RPC 37 V8 LTQ (ETD) Mascot Score: 61 73_sm15_14 #429 RT: 24.58 AV: 1 NL: 4.73E4 T: ITMS + c NSI d sa Full ms2 715.86@etd1. [.-.] 715.95.47 24 nce 22 18 16 14 12 8 Relative Abunda16 1171.31 6 912.24 42.39 4 2 855.25 444.24 56.44 675.46 1256.28 25.21 279.46 346.26 6.64 741.23 93.9 6 8 1414.43
(E)NGTNSAIANEQEEKpSEE(V) Pol III RPC 37 V8 LTQ (ETD) Mascot Score: 53 73_sm15_14 #488 RT: 29.25 AV: 1 NL: 1.84E3 T: ITMS + c NSI d sa Full ms2 965.76@etd1. [.-.] 966.7 14. 1832.94 1913.82 nce Relative Abunda 12 11 9 8 7 6 5 4 1186.38 3 943.19 1257.36 2 1 481.98 845.63 746.6 6.21 892.85 989.26 1116.35 1528.69 1642.71 167.59 1799.54 1758.79 6 8 16 18
(E)NGTNSAIANEQEEKpSEE(V) Pol III RPC 37 V8 LTQ (CID) Mascot Score: 71 73_sm15_14 #4879 RT: 29.24 AV: 1 NL: 6.26E3 T: ITMS + c NSI d w Full ms2 965.76@cid35. [255.-.] 916.62 dance Relative Abun 24 22 18 16 14 12 8 6 4 2 834.22 843.55 641.27 13.43 812.29 474.33 623.25 683.26 5.31 712.26 69.14 27.59 1174.46 1272.38 1358.56 1385.51 1486.51 1543.57 6 8 16 1657.7
(K)KTATEVpTPQEPK(H) Pol III RPC 19 Trypsin LTQ (CID) Mascot Score: 48 73_sm15_6 #4398 RT: 25.68 AV: 1 NL: 2.89E4 T: ITMS + c NSI d w Full ms2 47.43@cid35. [115.-1895.] 437.84 dance Relative Abun 24 22 18 16 14 12 8 6 4 2 299.84 357.31 431.91 531.36 598.36 653.39 244.2323 39.12 713.36 779.44 226.28 6.16 141.29 811.22 761.28 878.24 939.29 6 7 8 9
(K)KTATEVpTPQEPK(H) Pol III RPC 19 Trypsin LTQ (ETD) Mascot Score: 25 same precursor used as CID i.e. Consecutive scan 73_sm15_6 #4399 RT: 25.68 AV: 1 NL: 2.29E3 T: ITMS + c NSI d sa Full ms2 47.43@etd1. [.-.] 469.49 937.63 24 nce 22 18 16 14 12 8 Relative Abunda16 4. 637.24 75.7 779.34 922.45 6 357.11 14.22 522.12 856.37 991.33 53.36 4 1393.76 548.31 92.29 1264.38 2 247.8 318. 6 8
(K)HIQEEEEQDVDMpTGDEEQEEEPDREK(I) Pol III RPC 19 Trypsin LTQ (CID), 2+ ion Mascot Score: 115 73_sm15_6 #6123 RT: 37.42 AV: 1 NL: 6.26E3 T: ITMS + c NSI d w Full ms2 85.69@cid35. [285.-.] 52.65 nce Relative Abunda 45 35 25 15 5 432.35 361.24 626.42 93.3737 9.68 644. 796.13 1237. 1138.45 1352.58 1444.88 1494.8 1566.54 1589.7 184.88 6 8 16 18
(K)HIQEEEEQDVDMpTGDEEQEEEPDREK(I) Pol III RPC 19 Trypsin LTQ (ETD), 3+ ion scan immediately prior to CID scan (previous slide) Mascot Score: 56 73_sm15_6 #6122 RT: 37.41 AV: 1 NL: 1.77E3 T: ITMS + c NSI d sa Full ms2 814.49@etd1. [.-.] 813.54 1619.95 45 nce Relative Abunda 35 25 15 5 85.97 1563.25 1254. 525.38 1498. 396.19 912.52 1366.23 1644.71 654.32 1738.68 481.37 1853.5 612.34 6 8 16 18
(K)LKELAEDVDDApSTGDGAAK(G) Pol III RPC 8 Lys C LTQ (ETD) Mascot Score: 7 73_sm15_18 #6319 RT: 38.84 AV: 1 NL: 1.6E3 T: ITMS + c NSI d sa Full ms2 662.46@etd1. [.-.] 1986.37 Relative Abun dance 9 8 7 6 662.67 993.68 1713.64 445.17 963.63 1541.6. 1927.5 1383.63 273.27 63. 71.34 71.28 1285.31 915.51 1484.65 1656.54 4.94 461.38 6 8 16 18
(K)RKPNIILDEDDpTNDGIERYSDK(Y) Pol III RPC 8 Lys C LTQ (ETD) Mascot Score: 98 73_sm15_18 #7129 RT: 45.8 AV: 1 NL: 3.9E2 T: ITMS + c NSI d sa Full ms2 672.7@etd1. [.-.] 1327.93 Relative Abunda nce 9 8 7 6 246.19 671.31 896.55 1279.42 96.87 1221.81 18.54 513.35 17.75 1721.72 399.42 66.72 876.95 1359.88 198.15 6 8 16 18
(E)DFDVEHFpSDEE(T) Pol III RPB 6 V8 LTQ FT (CID) Mascot Score: 62 74_sm15_15 #4479 RT: 7.25 AV: 1 NL: 2.47E4 T: ITMS + c NSI d w Full ms2 724.75@cid35. [185.-146.] 675.78 dance Relative Abun 45 35 25 15 5 667.43 62.45 13. 11.34 874.33 1186. 378.15 973. 235.13 593. 743.21 843.38 277.13 449.22 996.76 1343.58 6 8
(E)DFDVEHFpSDEE(T) Pol III RPB 6 V8 LTQ (ETD) Mascot Score: 57 73_sm15_14 #9287 RT: 61.7 AV: 1 NL: 2.E3 T: ITMS + c NSI d sa Full ms2 725.3@etd1. [.-.] 724.8 24 nce 22 18 1318.45 16 14 12 1171.23 13.37 74.38 8 96. 1189.52 6 759.31 957.33 828. 4 54.87 11.8 2 312.13 396.13 537.82 66.8 987.44 6 8 Relative Abunda16 1432.42 148.55