(E)IEDGQDGGVpTPYSNE(S) Pol II RPB 1 Figure 5a in article V8 LTQ (CID) Mascot Score: 106

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1 (E)IEDGQDGGVpTPYSNE(S) Pol II RPB 1 Figure 5a in article V8 LTQ (CID) Mascot Score: 6 73_sm15_8 #734 RT: AV: 1 NL: 1.7E4 T: ITMS + c NSI d w Full ms2 [215.-.] dance Relative Abun

2 (E)IEDGQDGGVpTPYSNE(S) Pol II RPB 1 Figure 5b in article V8 LTQ (ETD) Mascot Score: 79 73_sm15_8 #71 RT: AV: 1 NL: 1.13E4 T: ITMS + c NSI d sa Full ms2 [.-.] Relative Abunda ance

3 (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 [5.-.] nce Relative Abunda

4 (Y)MPEQKITEIEDGQDGGVpTPY(S) Pol II RPB 1 Chymotrypsin LTQ (ETD) Mascot Score: 96 73_sm15_ #9853 RT: AV: 1 NL: 9.98E4 T: ITMS + c NSI d sa Full ms2 [.-.] dance Relative Abun

5 (E)LIAEEpSEDDSE(S) Pol II RPB 2 V8 LTQ FT (CID) Mascot Score: 49 74_sm15_13 #3143 RT: AV: 1 NL: 9.7E2 T: ITMS + c NSI d w Full ms2 [ ] nce Relative Abunda

6 (R)IRGNLMGKRVDFpSARpTVISGDPNLELDQVGVPK(S) Pol II RPB 3 Trypsin LTQ (CID) Mascot Score: 81 73_sm15_4b #8 RT: AV: 1 NL: 1.79E5 T: ITMS + c NSI d w Full ms2 [245.-.] Relative Abunda nce y3 y16 eliminates other possibilities

7 (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: AV: 1 NL: 1.89E5 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda z4 z16 eliminates other possibilities

8 (R)EASKDNVDFILp(SNVDLAMANS)LRR(V) Pol II RPB 3 Trypsin LTQ (CID) Mascot Score: 48 73_sm15_4b #12563 RT: AV: 1 NL: 8.84E3 T: ITMS + c NSI d w Full ms2 [2.-.] Relative Abunda nce b13, b14, b15 eliminate all other serines ETD spectra confirms was also next scan

9 (R)EASKDNVDFILSNVDLAMANpSLRR(V) Pol II RPB 3 Trypsin LTQ (ETD) Mascot Score: 53 73_sm15_4b #12564 RT: AV: 1 NL: 1.E4 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda16 c14, c15, c16 eliminate all other serines CID spectra confirms preceeding scan

10 (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 [ ] nce Relative Abunda

11 (E)DFDVEHFpSDEE(T) Pol II RPB 6 V8 LTQ (ETD) Mascot Score: 44 73_sm15_12 #11311 RT: AV: 1 NL: 9.88E3 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda

12 (K)SEGpSGSSLVQK(G) Pol III RPC 4 Trypsin LTQ FT (CID) Mascot Score: 58 74_sm15_3 #1724 RT: AV: 1 NL: 1.47E3 T: ITMS + c NSI d w Full ms2 [ ] nce Relative Abunda

13 (K)SEGpSGSSLVQK(G) Pol III RPC 4 Trypsin LTQ (ETD) Mascot Score: 55 73_sm15_6 #494 RT: AV: 1 NL: 7.27E3 T: ITMS + c NSI d sa Full ms2 [.-.] dance Relative Abun

14 (R)NLIEDEDDGEpSEK(S) Pol III RPC 4 Trypsin LTQ FT (CID) Mascot Score: 51 74_sm15_3 #3489 RT: AV: 1 NL: 7.38E2 T: ITMS + c NSI d w Full ms2 [ ] Relative Abunda nce

15 (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 [.-.] Relative Abunda nce

16 (K)KNIKKKDpTKDALSTRELAGK(V) Pol III RPC 4 Lys C LTQ (ETD) Mascot Score: 47 73_sm15_18 #5556 RT: AV: 1 NL: 1.51E4 T: ITMS + c NSI d sa Full ms2 [.-19.] Relative Abunda nce z2 z9 suggests T8 6 8

17 (K)RSGpSNAAASLPSK(K) Pol III RPC 3 Lys C LTQ (ETD) Mascot Score: 81 73_sm15_18 #4589 RT: AV: 1 NL: 2.74E3 T: ITMS + c NSI d sa Full ms2 [ ] Relative Abunda nce

18 (E)VKAEDDpTGEEEE(D) Pol III RPC 37 V8 LTQ FT (CID) Mascot Score: 51 74_sm15_15 #1113 RT: AV: 1 NL: 7.78E2 T: ITMS + c NSI d w Full ms2 [ ] nce Relative Abunda

19 (E)VKAEDDpTGEEEE(D) Pol III RPC 37 V8 LTQ (ETD) Mascot Score: 61 73_sm15_14 #429 RT: AV: 1 NL: 4.73E4 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda

20 (E)NGTNSAIANEQEEKpSEE(V) Pol III RPC 37 V8 LTQ (ETD) Mascot Score: 53 73_sm15_14 #488 RT: AV: 1 NL: 1.84E3 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda

21 (E)NGTNSAIANEQEEKpSEE(V) Pol III RPC 37 V8 LTQ (CID) Mascot Score: 71 73_sm15_14 #4879 RT: AV: 1 NL: 6.26E3 T: ITMS + c NSI d w Full ms2 [255.-.] dance Relative Abun

22 (K)KTATEVpTPQEPK(H) Pol III RPC 19 Trypsin LTQ (CID) Mascot Score: 48 73_sm15_6 #4398 RT: AV: 1 NL: 2.89E4 T: ITMS + c NSI d w Full ms2 [ ] dance Relative Abun

23 (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: AV: 1 NL: 2.29E3 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda

24 (K)HIQEEEEQDVDMpTGDEEQEEEPDREK(I) Pol III RPC 19 Trypsin LTQ (CID), 2+ ion Mascot Score: _sm15_6 #6123 RT: AV: 1 NL: 6.26E3 T: ITMS + c NSI d w Full ms2 [285.-.] nce Relative Abunda

25 (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: AV: 1 NL: 1.77E3 T: ITMS + c NSI d sa Full ms2 [.-.] nce Relative Abunda

26 (K)LKELAEDVDDApSTGDGAAK(G) Pol III RPC 8 Lys C LTQ (ETD) Mascot Score: 7 73_sm15_18 #6319 RT: AV: 1 NL: 1.6E3 T: ITMS + c NSI d sa Full ms2 [.-.] Relative Abun dance

27 (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 [.-.] Relative Abunda nce

28 (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 [ ] dance Relative Abun

29 (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 [.-.] nce Relative Abunda