Mascot Search Results

Mascot Search Results Spot 746

User : A.Srinivasan

Email : [email protected] Search title : D:\PE Sciex Data\Projects\Default\Data\Data lo kala spot 1lo kala spot 1.wiff (sample number 1) MS data file : C:\Temp\mas4D.tmp Database : MSDB 20060831 (3239079 sequences; 1079594700 residues) Taxonomy : Homo sapiens (human) (148148 sequences) Timestamp : 4 Apr 2008 at 11:16:29 GMT Protein hits LPHUA1 apolipoprotein A-I precursor [validated] - human : CAC399 Sequence 7 from Patent EP1101772.- Homo sapiens (Human). 60

Q8WWZ8 LZP (PPFL826) (CDNA FLJ39116 fis, clone NTONG2006301, highly _HUMAN similar to Mus musculus EF-9 mRNA).- Homo sapiens (Human). Q86TH5 ARFGEF2 protein (Fragment).- Homo sapiens (Human). _HUMAN PC2205 interferon-alpha LCA-2b binding subtype - human (fragment)

Probability Based Mowse Score

Ions score is -10*Log(P), where P is the probability that the observed match is a random event. Individual ions scores > 40 indicate identity or extensive homology (p<0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits.

Peptide Summary Report

Format As Peptide Summary Help Significance threshold p< 5 0.05 Max. number of hits

Standard scoring MudPIT Ions score or expect cut-off Show sub-sets 0 0 scoring

Show pop-ups Suppress pop- Sort unassigned Require bold red Decreasing Score ups

Search Selected Error tolerant

LPHUA1 Mass: 30759 Score: 314 Queries 1. matched: 28 emPAI: 4.69 apolipoprotein A-I precursor [validated] - human Check to include this hit in error tolerant search

Query Observe Mr(expt Mr(calc Mis Scor Expec Ran Delta Peptide d ) ) s e t k - 416.218 830.421 830.428 11 0.007 0 23 5.3 1 R.LAEYHAK.A 0 5 6 2 - 435.246 868.478 868.513 21 0.034 1 15 19 1 R.QKVEPLR.A 5 4 0 7 - 437.216 872.417 872.435 22 0.017 0 48 0.015 1 R.AELQEGAR.Q 2 9 2 3 - 448.236 894.458 895.476 25 1.017 0 (19) 9.8 1 K.LHELQEK.L 5 5 3 8 - 448.738 895.463 895.476 26 0.013 0 27 1.3 1 K.LHELQEK.L 8 1 3 2 - 506.787 1011.56 1011.57 44 0.011 0 34 0.26 1 K.AKPALEDLR.Q 4 02 13 0 - 516.260 1030.50 1030.51 0.007 47 0.005 0 50 1 K.LSPLGEEMR.D 6 67 17 3 0 524.755 1047.49 1046.50 0.990 K.LSPLGEEMR.D + 53 0 (33) 0.34 1 8 71 66 5 Oxidation (M) - 607.836 1213.65 1214.61 69 0.956 0 40 0.063 1 K.ATEHLSTLSEK.A 0 74 43 8 - 405.874 1214.60 1214.61 70 0.011 0 (36) 0.17 1 K.ATEHLSTLSEK.A 9 29 43 4 - 615.847 1229.68 1229.70 0.006 73 0.021 0 50 1 R.QGLLPVLESFK.V 6 07 20 6 3 - 618.344 1234.67 1234.68 75 0.007 0 47 0.015 1 K.DLATVYVDVLK.D 1 36 09 3 642.295 1282.57 1282.56 0.011 85 0 34 0.22 1 K.WQEEMELYR.Q 8 70 52 8 650.291 1298.56 1298.56 0.008 1.1e+ K.WQEEMELYR.Q + 91 0 (7) 1 6 86 01 5 02 Oxidation (M) - 434.202 1299.58 1300.64 92 1.054 0 37 0.12 1 R.THLAPYSDELR.Q 7 63 11 9 - 434.550 1300.62 1300.64 93 0.011 0 (34) 0.22 1 R.THLAPYSDELR.Q 5 96 11 5 - 460.900 1379.67 1379.70 109 0.029 1 (11) 50 1 K.VQPYLDDFQKK.W 2 88 85 8 461.244 1380.71 1379.70 1.002 110 1 14 23 1 K.VQPYLDDFQKK.W 4 14 85 9 - 693.854 1385.69 1385.70 9.5e- 111 0.013 0 68 1 K.VSFLSALEEYTK.K 2 39 78 05 9 - 467.209 1398.60 1399.66 113 1.056 0 (15) 18 1 R.DYVSQFEGSALGK.Q 0 52 20 7 700.840 1399.66 1399.66 0.004 114 0 47 0.011 1 R.DYVSQFEGSALGK.Q 3 61 20 2 471.256 1410.74 1410.66 0.086 117 1 19 7.1 1 K.KWQEEMELYR.Q 2 69 01 7 - 476.554 1426.64 1426.65 K.KWQEEMELYR.Q + 119 0.014 1 (8) 84 5 1 06 51 Oxidation (M) 5 - 488.286 1461.83 1461.84 123 0.006 1 36 0.13 1 R.VKDLATVYVDVLK.D 4 74 43 8 - 806.888 1611.76 1611.77 1.7e- 133 0.015 0 85 1 K.LLDNWDSVTSTFSK.L 8 30 81 06 0 645.314 1932.92 1931.92 0.994 3.7e+ 143 0 1 4 R.EQLGPVTQEFWDNLEK.E 3 11 65 6 02 - 734.699 2201.07 2201.11 K.LREQLGPVTQEFWDNLEK. 152 0.035 1 44 0.014 1 2 57 17 E 9 735.029 2202.06 2201.11 0.955 K.LREQLGPVTQEFWDNLEK. 153 1 (32) 0.26 1 6 68 17 2 E

Proteins matching the same set of peptides: CAA00975 Mass: 28061 Score: 314 Queries matched: 28 APOA1 PROTEIN (FRAGMENT).- Homo sapiens (Human). AAA51747 Mass: 28944 Score: 314 Queries matched: 28 HUMAPOAIC NID: - Homo sapiens Mascot Search Results Spot 114

User : A.Srinivasan Email : [email protected] Search title : D:\PE Sciex Data\Projects\Default\Data\Data lo kala spot 2alo kala spot 2a.wiff (sample number 1) MS data file : C:\Temp\mas15.tmp Database : MSDB 20060831 (3239079 sequences; 1079594700 residues) Taxonomy : Homo sapiens (human) (148148 sequences) Timestamp : 17 Apr 2008 at 13:10:07 GMT Protein LPHUA1 apolipoprotein A-I precursor [validated] - human hits : Q4EW67_ADE0 Hexon protein (Fragment).- Human adenovirus 9 9 (HAdV-9). Q3KQZ0_HUMA NUP214 protein.- Homo sapiens (Human). N K1688_HUMAN Protein KIAA1688.- Homo sapiens (Human). BAA20829 AB002372 NID: - Homo sapiens

Format As Peptide Summary Help

Significance threshold p< 5 0.05 Max. number of hits Standard scoring MudPIT Ions score or expect cut-off Show sub-sets 0 0 scoring

1. LPHUA1 Mass: 30759 Score: 114 Queries matched: 8 apolipoprotein A-I precursor [validated] - human Check to include this hit in error tolerant search

Query ObserveMr(expt) Mr(calc) Mis Scor Expec Ran Delta Peptide d s e t k - 437.211872.4088 872.4352 9 0.026 0 16 21 2 R.AELQEGAR.Q 7 3 516.2861030.5581030.511 0.046 17 0 (15) 25 1 K.LSPLGEEMR.D 5 5 7 8 524.3221046.6291046.506 0.123 K.LSPLGEEMR.D + 20 0 15 23 1 2 8 6 2 Oxidation (M) - 626.8051251.5951251.613 25 0.017 0 22 3.7 1 K.VQPYLDDFQK.K 2 8 6 7 642.3071282.6001282.565 0.035 1.1e+ 27 0 8 2 K.WQEEMELYR.Q 6 7 2 5 02 434.8881301.6421300.641 1.001 29 0 24 2.5 1 R.THLAPYSDELR.Q 1 5 1 4 701.3391400.6641399.662 1.002 36 0 12 35 2 R.DYVSQFEGSALGK.Q 3 1 0 2 807.3851612.7561611.778 0.978 38 0 18 7.8 1 K.LLDNWDSVTSTFSK.L 3 0 1 0

Proteins matching the same set of peptides: CAA00975 Mass: 28061 Score: 114 Queries matched: 8 APOA1 PROTEIN (FRAGMENT).- Homo sapiens (Human). AAA35545 Mass: 30745 Score: 114 Queries matched: 8 HUMAPOAIP NID: - Homo sapiens AAA51747 Mass: 28944 Score: 114 Queries matched: 8 HUMAPOAIC NID: - Homo sapiens Mascot Search Results Spot 816

User : A.Srinivasan Email : [email protected] Search title : D:\PE Sciex Data\Projects\Default\Data\Data lo kala spot 3lo kala spot 3.wiff (sample number 1) MS data file : C:\Temp\masA.tmp Database : MSDB 20060831 (3239079 sequences; 1079594700 residues) Taxonomy : Homo sapiens (human) (148148 sequences) Timestamp : 11 Apr 2008 at 09:52:34 GMT Protein 1QABE retinol binding protein, chain E - human hits :

Q5JVP6_HU Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6.- MAN Homo sapiens (Human). Sequence 1 from Patent WO0206331.- Homo sapiens CAD38234 (Human). AAD33397 AF128881 NID: - Homo sapiens Q86TH5_HU ARFGEF2 protein (Fragment).- Homo sapiens (Human). MAN

Significance threshold p< 5 0.05 Max. number of hits Ions score or expect cut-off Show sub-sets Standard scoring MudPIT 0 0 scoring

1. 1QABE Mass: 20745 Score: 47 Queries matched: 6 emPAI: 0.66 retinol binding protein, chain E - human Check to include this hit in error tolerant search

Query ObserveMr(expt) Mr(calc) Mis Scor Expec Ran Delta Peptide d s e t k 581.262 1160.510 1160.532 - 140 0 23 3.7 1 R.FSGTWYAMAK.K 3 0 5 0.0225 599.807 1197.601 1197.618 - 145 0 31 0.46 1 K.YWGVASFLQK.G 9 3 2 0.0169 434.892 1301.655 1302.613 - 168 0 36 0.17 1 R.LIVHNGYCDGR.S 5 8 9 0.9581 435.224 1302.653 1302.613 169 0.0391 0 (29) 0.9 1 R.LIVHNGYCDGR.S 9 0 9 435.537 1303.591 1302.613 171 0.9780 0 (18) 11 1 R.LIVHNGYCDGR.S 9 9 9 688.973 2063.898 2063.962 - R.LLNLDGTCADSYSFV 229 0 19 4.5 1 4 5 3 0.0638 FSR.D

Proteins matching the same set of peptides: VAHU Mass: 23195 Score: 47 Queries matched: 6 plasma retinol-binding protein precursor [validated] - human Q5VY30_HUMAN Mass: 23271 Score: 47 Queries matched: 6 Retinol binding protein 4, plasma.- Homo sapiens (Human). AAH20633 Mass: 23371 Score: 47 Queries matched: 6 BC020633 NID: - Homo sapiens CAH72328 Mass: 23337 Score: 47 Queries matched: 6 AL356214 NID: - Homo sapiens Mascot Search Results Spot 1051

User : A.Srinivasan Email : [email protected] Search title : D:\PE Sciex Data\Projects\Default\Data\Data lo kala spot 9lo kala spot 9.wiff (sample number 1) MS data file : C:\Temp\mas57.tmp Database : MSDB 20060831 (3239079 sequences; 1079594700 residues) Taxonomy : Homo sapiens (human) (148148 sequences) Timestamp : 7 Apr 2008 at 06:57:42 GMT Protein alpha-1-acid glycoprotein 1 precursor [validated] - OMHU1 hits : human OMHU2 alpha-1-acid glycoprotein 2 precursor - human CAE98367 AX884253 NID: - Homo sapiens ALPHA1-ACID GLYCOPROTEIN (FRAGMENT).- Homo sapiens BAA34292 (Human). Q9UL10_HUM Hypothetical protein SARDH.- Homo sapiens (Human). AN

Significance threshold p< 5 0.05 Max. number of hits

Show pop-ups Suppress pop- Sort unassigned Require bold red Decreasing Score ups Search Selected Error tolerant

1. OMHU1 Mass: 23725 Score: 166 Queries matched: 13 emPAI: 1.84 alpha-1-acid glycoprotein 1 precursor [validated] - human Check to include this hit in error tolerant search

QuerObserve Mr(expt Mr(calc Mis Scor Expec Ran Delta Peptide y d ) ) s e t k 404.200 806.385 805.345 1.040 19 1 11 69 8 R.KQEEGES.- 0 4 4 1 497.765 993.516 993.513 0.003 49 0 (54) 0.003 1 K.TEDTIFLR.E 7 8 1 7 497.900 993.785 993.513 0.272 0.001 50 0 54 1 K.TEDTIFLR.E 0 4 1 3 7 - 509.257 1016.50 1017.48 54 0.979 1 29 0.95 1 K.DKCEPLEK.Q 4 02 01 8 - 509.744 1017.47 1017.48 55 0.006 1 (21) 6.2 1 K.DKCEPLEK.Q 1 36 01 4 - 556.761 1111.50 1111.51 71 0.010 0 42 0.039 1 K.SDVVYTDWK.K 3 81 86 5 - 580.796 1159.57 1159.58 80 0.002 0 47 0.015 1 K.WFYIASAFR.N 8 91 15 3 723.370 1444.72 1444.65 0.071 120 0 42 0.035 1 K.TYMLAFDVNDEK.N 0 54 44 0 731.346 1460.67 1460.64 0.029 K.TYMLAFDVNDEK.N + 122 0 (10) 53 1 8 90 93 7 Oxidation (M) - 570.282 1707.82 1707.84 134 0.020 0 26 1.2 1 K.NWGLSVYADKPETTK.E 8 65 68 3 872.392 1742.77 1741.79 0.972 8.3e- 137 0 68 1 K.EQLGEFYEALDCLR.I 6 07 81 5 05 439.245 1752.95 1751.94 1.004 139 0 13 24 1 R.YVGGQEHFAHLLILR.D 2 16 71 5 784.636 3134.51 3134.49 0.025 K.TYMLAFDVNDEKNWGLSVYA 166 1 20 2.6 1 3 61 06 5 DKPETTK.E

Proteins matching the same set of peptides: Q5T539_HUMAN Mass: 23753 Score: 166 Queries matched: 13 Orosomucoid 1.- Homo sapiens (Human). CAA29229 Mass: 23579 Score: 166 Queries matched: 13 HSA1GPA1 NID: - Homo sapiens Mascot Search Results Spot 129

User : A.Srinivasan Email : [email protected] Search title : D:\PE Sciex Data\Projects\Default\Data\Data lo kala spot 6lo kala spot 6.wiff (sample number 1) MS data file : C:\Temp\mas58.tmp Database : MSDB 20060831 (3239079 sequences; 1079594700 residues) Taxonomy : Homo sapiens (human) (148148 sequences) Timestamp : 7 Apr 2008 at 07:19:29 GMT Protein ITHUC1 complement C1 inhibitor precursor [validated] - human hits : alpha-1-acid glycoprotein 1 precursor [validated] - OMHU1 human CAE9836 AX884253 NID: - Homo sapiens 7 CAF0077 AX886632 NID: - Homo sapiens 0 AAQ8912 AY358765 NID: - Homo sapiens 5

Significance threshold p< 5 0.05 Max. number of hits Ions score or expect cut-off Show sub-sets Standard scoring MudPIT scoring 0 0

ITHUC1 Mass: 55347 Score: 190 Queries 1. matched: 22 emPAI: 0.80 complement C1 inhibitor precursor [validated] - human Check to include this hit in error tolerant search

QuerObserve Mr(expt Mr(calc Mis Scor Expec Ran Delta Peptide y d ) ) s e t k - 591.300 590.292 590.309 6.4e+ 17 0.017 0 2 6 K.AIMEK.L 0 7 8 02 0 404.199 806.383 805.382 1.001 27 0 (16) 21 2 K.VPMMNSK.K 2 9 6 2 412.203 822.392 821.377 1.014 K.VPMMNSK.K + Oxidation 32 0 23 3.1 1 4 3 5 7 (M) 427.254 852.494 852.431 0.063 36 0 14 27 1 K.FPVFMGR.V 7 8 6 2 455.736 909.457 909.455 0.002 48 0 25 2.2 1 R.TLYSSSPR.V 1 6 6 1 468.226 934.438 934.437 0.001 54 0 11 69 1 R.MEPFHFK.N 6 7 1 6 534.275 1066.53 1066.52 0.009 82 0 12 56 1 K.LYHAFSAMK.K 5 65 70 6 534.767 1067.52 1066.52 0.993 1.1e+ 83 0 (9) 2 K.LYHAFSAMK.K 5 05 70 6 02 542.297 1082.57 1082.52 0.057 2.9e+ K.LYHAFSAMK.K + 86 0 (3) 6 0 93 19 5 02 Oxidation (M) 558.800 1115.58 1115.58 0.004 0.006 91 0 50 1 R.LLDSLPSDTR.L 5 64 22 2 5 593.353 1184.69 1184.69 0.000 107 0 25 2.3 1 K.FQPTLLTLPR.I 2 19 17 2 - 609.800 1217.58 1217.58 116 0.000 0 (9) 91 2 K.DFTCVHQALK.G 0 54 63 9 406.876 1217.60 1217.58 0.020 117 0 (11) 52 3 K.DFTCVHQALK.G 2 68 63 5 407.205 1218.59 1217.58 1.007 118 0 18 10 1 K.DFTCVHQALK.G 3 41 63 8 632.846 1263.67 1263.67 0.007 127 0 75 2e-05 1 K.TNLESILSYPK.D 5 85 10 5 659.412 1316.81 1316.80 0.004 0.000 139 0 62 1 R.LVLLNAIYLSAK.W 7 09 67 2 44 478.260 1431.75 1430.75 1.003 153 0 28 0.92 1 K.YPVAHFIDQTLK.A 2 89 58 1 - 749.360 1496.70 1497.70 K.VTTSQDMLSIMEK.L + 159 0.999 0 38 0.083 1 2 58 55 Oxidation (M) 6 575.310 1722.91 1722.88 0.021 169 1 24 2.1 1 R.IKVTTSQDMLSIMEK.L 8 05 96 0 609.800 1826.37 1825.96 0.409 176 0 39 0.038 1 K.GVTSVSQIFHSPDLAIR.D 0 82 87 5 610.001 1826.98 1825.96 1.013 177 0 (23) 2.3 1 K.GVTSVSQIFHSPDLAIR.D 4 24 87 8 872.799 2615.37 2614.39 0.982 R.TLLVFEVQQPFLFVLWDQQHK 196 0 43 0.015 1 7 72 48 4 .F

Proteins matching the same set of peptides: AAA35613 Mass: 55375 Score: 190 Queries matched: 22 HUMC1INHA NID: - Homo sapiens AAB59387 Mass: 55346 Score: 190 Queries matched: 22 HUMC1INHB NID: - Homo sapiens Mascot Search Results Spot 954

User : JITENDRA VASHIST Email : [email protected] Search title : H:\mass res\LOKESH 31.5.10\TTR1.wiff (sample number 1) MS data file : C:\DOCUME~1\DRAF40~1.JIT\LOCALS~1\Temp\mas18.tmp Database : NCBInr 20100724 (11505486 sequences; 3925745078 residues) Taxonomy : Homo sapiens (human) (232657 sequences) Timestamp : 27 Jul 2010 at 02:17:25 GMT Protein gi| hits 12603 Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin : 0594 gi| 51077 Chain A, Leu 55 Pro Transthyretin Crystal Structure 91 gi| Chain A, An Engineered Transthyretin Monomer That Is Non- 17942 Amyloidogenic - Unless Partially Denatured 890 gi| Chain 1, The X-Ray Crystal Structure Refinements Of Normal Human 25904 Transthyretin And The Amyloidogenic Val 30-->met Variant To 1.7 5651 Angstroms Resolution gi| 43547 cytokeratin 9 [Homo sapiens] 6

Mascot Score Histogram Ions score is -10*Log(P), where P is the probability that the observed match is a random event. Individual ions scores > 42 indicate identity or extensive homology (p<0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits.

1. gi|126030594 Mass: 13761 Score: 449 Matches: 13(9) Sequences: 12(9) emPAI: 14.81 Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin Check to include this hit in error tolerant search

QuerObserveMr(exptMr(calc DeltMis ScoExpecRan Uniq Peptide y d ) ) a s re t k ue 635.3541268.691267.641.050 0.008 451 1 51 1 K.VEIDTKSYWK.A 8 51 48 2 2 683.8951365.771365.750.024 7.5e- 503 0 71 1 R.GSPAINVAVHVFR.K 5 64 17 6 05 - 697.3701392.721393.61 2.3e- 510 0.8880 86 1 K.AADDTWEPFASGK.T 7 68 50 06 2 492.2781473.811473.740.064 -.GPTGTGESKGPLMVK.V + 549 1 18 17 1 U 6 40 97 2 Oxidation (M) 747.9381493.861493.840.015 8.5e- 560 1 90 1 R.GSPAINVAVHVFRK.A 3 21 67 4 07 761.8771521.741521.710.031 571 1 97 2e-07 1 R.KAADDTWEPFASGK.T 9 12 00 2 - 526.2701575.791576.75 -.GPTGTGESKCPLMVK.V + 594 0.9681 32 0.52 1 U 9 09 89 Oxidation (M) 0 1181.132360.242359.231.016 R.YTIAALLSPYSYSTTAVVTN 654 0 43 0.031 1 12 78 11 7 PK.E 818.1042451.292450.191.093 1.8e- K.ALGISPFHEHAEVVFTANDS 662 0 85 1 3 11 79 2 06 GPR.R 819.4102455.212454.141.067 8.9e- K.TSESGELHGLTTEEEFVEGI 664 0 68 1 9 09 38 1 05 YK.V 819.4192455.232454.141.093 (12 K.TSESGELHGLTTEEEFVEGI 666 0 35 1 7 72 38 4 ) YK.V 830.7862489.332488.271.064 R.YTIAALLSPYSYSTTAVVTN 673 1 19 6.5 1 8 86 37 9 PKE.- 839.7992516.372515.331.043 1.2e- R.RYTIAALLSPYSYSTTAVVT 674 1 76 1 3 61 22 9 05 NPK.E Mascot Search Results Spot 958

User : JITENDRA VASHIST Email : [email protected] Search title : H:\mass res\LOKESH 31.5.10\TTR1A.wiff (sample number 1) MS data file : C:\DOCUME~1\DRAF40~1.JIT\LOCALS~1\Temp\mas1B.tmp Database : NCBInr 20100724 (11505486 sequences; 3925745078 residues) Taxonomy : Homo sapiens (human) (232657 sequences) Timestamp : 27 Jul 2010 at 02:25:42 GMT Protein gi| hits 12603 Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin : 0594 gi| 51077 Chain A, Leu 55 Pro Transthyretin Crystal Structure 91 gi| Chain A, An Engineered Transthyretin Monomer That Is Non- 17942 Amyloidogenic - Unless Partially Denatured 890 gi| 11431 transthyretin [Homo sapiens] 9005 gi| Chain 1, The X-Ray Crystal Structure Refinements Of Normal Human 25904 Transthyretin And The Amyloidogenic Val 30-->met Variant To 1.7 5651 Angstroms Resolution

Mascot Score Histogram Ions score is -10*Log(P), where P is the probability that the observed match is a random event. Individual ions scores > 42 indicate identity or extensive homology (p<0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits.

1. gi|126030594 Mass: 13761 Score: 503 Matches: 12(10) Sequences: 9(7) emPAI: 6.45 Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin Check to include this hit in error tolerant search

Quer Observe Mr(expt Mr(calc Delt Mis Sco Expec Ran Uniq Peptide y d ) ) a s re t k ue 683.895 1365.77 1365.75 0.024 3.5e- 462 0 74 1 R.GSPAINVAVHVFR.K 1 57 17 0 05 684.391 1366.76 1365.75 1.017 (48 463 0 0.019 1 R.GSPAINVAVHVFR.K 6 87 17 0 ) - 692.388 1382.76 1383.82 K.KPLMVKVLDAVR.G + 470 1.065 1 23 5.2 1 U 3 21 72 Oxidation (M) 1 697.824 1393.63 1393.61 0.020 9.6e- 473 0 80 1 K.AADDTWEPFASGK.T 9 52 50 2 06 747.944 1493.87 1493.84 0.028 7.8e- 515 1 71 1 R.GSPAINVAVHVFRK.A 8 50 67 3 05 761.873 1521.73 1521.71 0.022 131 7.3e- 524 1 1 R.KAADDTWEPFASGK.T 5 24 00 5 11 1181.13 2360.24 2359.23 1.017 R.YTIAALLSPYSYSTTAVVT 600 0 40 0.057 1 16 87 11 6 NPK.E 818.092 2451.25 2450.19 1.056 1.7e- K.ALGISPFHEHAEVVFTAND 606 0 75 2 2 47 79 8 05 SGPR.R 819.405 2455.19 2454.14 1.050 (44 K.TSESGELHGLTTEEEFVEG 607 0 0.02 1 2 39 38 1 ) IYK.V 819.405 2455.19 2454.14 1.051 (47 K.TSESGELHGLTTEEEFVEG 608 0 0.011 1 6 51 38 3 ) IYK.V 819.406 2455.19 2454.14 1.054 4.6e- K.TSESGELHGLTTEEEFVEG 609 0 71 1 6 79 38 1 05 IYK.V 839.796 2516.36 2515.33 1.036 1.7e- R.RYTIAALLSPYSYSTTAVV 618 1 84 1 8 85 22 3 06 TNPK.E Mascot Search Results Spot 1050

User : JITENDRA VASHIST Email : [email protected] Search title : H:\mass res\LOKESH 31.5.10\TTR2.wiff (sample number 1) MS data file : C:\DOCUME~1\DRAF40~1.JIT\LOCALS~1\Temp\mas1D.tmp Database : NCBInr 20100724 (11505486 sequences; 3925745078 residues) Taxonomy : Homo sapiens (human) (232657 sequences) Timestamp : 27 Jul 2010 at 02:36:19 GMT Protein gi| keratin 1 [Homo sapiens] hits : 7331218 gi| prealbumin [Homo sapiens] 219978 gi| Chain A, An Engineered Transthyretin Monomer That Is Non- 1794289 Amyloidogenic - Unless Partially Denatured 0 gi| cytokeratin 9 [Homo sapiens] 435476 gi| unnamed protein product [Homo sapiens] 28317

Mascot Score Histogram

Ions score is -10*Log(P), where P is the probability that the observed match is a random event. Individual ions scores > 43 indicate identity or extensive homology (p<0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. Peptide Summary Report

1. gi|7331218 Mass: 66149 Score: 190 Matches: 12(7) Sequences: 10 (6) emPAI: 0.73 keratin 1 [Homo sapiens] Check to include this hit in error tolerant search

Quer Observ Mr(expt Mr(calc Delt MisScor Expec Ran Uniq Peptide y ed ) ) a s e t k ue 487.29 972.565 972.524 0.04 0.001 271 0 60 1 K.IEISELNR.V 01 7 0 17 3 517.28 1032.55 1032.50 0.04 325 0 32 0.86 1 U R.TLLEGEESR.M 58 70 87 82 590.33 1178.64 1178.59 0.05 0.000 407 0 62 1 K.YEELQITAGR.H 00 54 31 22 77 633.35 1264.69 1264.62 0.06 0.009 461 0 50 1 U R.TNAENEFVTIK.K 33 20 99 21 9 650.80 1299.58 1299.52 0.06 482 0 (47) 0.02 1 U K.NMQDMVEDYR.N 07 69 24 45 651.88 1301.75 1301.70 0.05 0.003 485 0 54 1 U R.SLDLDSIIAEVK.A 68 91 78 13 7 658.79 1315.57 1315.51 0.05 K.NMQDMVEDYR.N + 500 0 50 0.012 1 U 39 32 73 59 Oxidation (M) 666.79 1331.57 1331.51 0.05 K.NMQDMVEDYR.N + 2 512 0 (26) 3 1 U 29 13 22 91 Oxidation (M) 679.37 1356.74 1356.68 0.05 0.000 523 0 65 1 U K.LNDLEDALQQAK.E 77 09 85 25 33 738.41 1474.81 1474.77 0.03 574 0 26 2.7 1 R.FLEQQNQVLQTK.W 58 71 80 91 858.94 1715.88 1715.84 0.03 621 0 34 0.3 1 U K.QISNLQQSISDAEQR.G 78 10 38 72 584.62 1750.85 1750.81 0.03 R.GSGGGSSGGSIGGRGSSSG 625 1 6 2e+02 10 U 39 00 95 05 GVK.S

Proteins matching the same set of peptides: gi|11935049 Mass: 66198 Score: 190 Matches: 12(7) Sequences: 1

0(6) keratin 1 [Homo sapiens] gi|119395750 Mass: 66170 Score: 190 Matches: 12(7) Sequences: 10

(6) keratin, type II cytoskeletal 1 [Homo sapiens] gi|219978 Mass: 16023 Score: 188 Matches: 5(3) Sequences: 5(3) emPAI: 1.39 prealbumin [Homo sapiens] Check to include this hit in error tolerant search

Quer Observ Mr(expt Mr(calc Delt MisScor Expec Ran Uniq Peptide y ed ) ) a s e t k ue 635.35 1268.70 1267.64 1.055 467 1 5 3e+02 2 K.VEIDTKSYWK.A 75 04 48 5 - 697.37 1392.74 1393.61 2.7e- 550 0.874 0 96 1 K.AADDTWEPFASGK.T 76 07 50 07 3 761.88 1521.74 1521.71 0.038 588 1 30 0.87 1 R.KAADDTWEPFASGK.T 14 83 00 3 818.10 2451.30 2450.19 1.106 0.000 K.ALGISPFHEHAEVVFT 659 0 59 1 U 86 40 79 1 65 ANDSGPR.R 819.41 2455.22 2454.14 1.081 6.4e- K.TSESGELHGLTTEEEF 660 0 79 1 58 55 38 7 06 VEGIYK.V

Proteins matching the same set of peptides: gi|386998 Mass: 15932 Score: 188 Matches: 5(3) Sequences:

5(3) prealbumin [Homo sapiens] gi|443295 Mass: 13810 Score: 188 Matches: 5(3) Sequences: 5(3

) Chain A, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val30met Variant To 1.7 Angstroms Resolution gi|443297 Mass: 13840 Score: 188 Matches: 5(3) Sequences: 5(3 ) Chain A, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val30met Variant To 1.7 Angstroms Resolution gi|443299 Mass: 13842 Score: 188 Matches: 5(3) Sequences: 5(3

) Chain A, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val30met Variant To 1.7 Angstroms Resolution gi|1827569 Mass: 13824 Score: 188 Matches: 5(3) Sequences:

5(3) Chain A, Transthyretin-V122I CARDIOMYOPATHIC MUTANT gi|2098255 Mass: 13806 Score: 188 Matches: 5(3) Sequences: 5

(3) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|3891451 Mass: 13711 Score: 188 Matches: 5(3) Sequences:

5(3) Chain A, Transthyretin (Del Val122) gi|3891560 Mass: 13840 Score: 188 Matches: 5(3) Sequences: 5

(3) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|3891562 Mass: 13840 Score: 188 Matches: 5(3) Sequences: 5

(3) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|4507725 Mass: 15991 Score: 188 Matches: 5(3) Sequences:

5(3) transthyretin precursor [Homo sapiens] gi|14719497 Mass: 12671 Score: 188 Matches: 5(3) Sequences

: 5(3) Chain A, Transthyretin Thr119met Protein Stabilisation gi|27065112 Mass: 13807 Score: 188 Matches: 5(3) Sequences:

5(3) Chain A, Crystal Structure Of The Transthyretin Mutant Ttr Y114c- Data Collected At Room Temperature gi|31615374 Mass: 13718 Score: 188 Matches: 5(3) Sequences

: 5(3) Chain A, Crystal Structure Of The Transthyretin Mutant Ttr C10aY114C gi|48145933 Mass: 15977 Score: 188 Matches: 5(3) Sequences

: 5(3) TTR [Homo sapiens] gi|50513594 Mass: 13918 Score: 188 Matches: 5(3) Sequences:

5(3) Chain A, Crystal Structure Of The Transthyretin Mutant A108yL110E Solved In Space Group P21212 gi|55669575 Mass: 12836 Score: 188 Matches: 5(3) Sequences

: 5(3) Chain A, A Covalent Dimer Of Transthyretin That Affects The Amyloid Pathway gi|62738388 Mass: 13791 Score: 188 Matches: 5(3) Sequences:

5(3) Chain A, Structure Of Ttr R104h: A Non-Amyloidogenic Variant With Protective Clinical Effects gi|73535906 Mass: 13941 Score: 188 Matches: 5(3) Sequences

: 5(3) Chain A, Crystal Structure Of Human Transthyretin With Bound Iodide gi|114319005 Mass: 15062 Score: 188 Matches: 5(3) Sequence

s: 5(3) transthyretin [Homo sapiens] gi|212374952 Mass: 13798 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Crystal Structure Of Transthyretin Variant V20s gi|223674041 Mass: 13456 Score: 188 Matches: 5(3) Sequences

: 5(3) Chain A, Crystal Structure Of Transthyretin In Complex With Iododiflunisal-Betaalaome gi|224510585 Mass: 12996 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Crystal Structure Of The Apo Form Of Human Wild-Type Transthyretin gi|226438187 Mass: 13784 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Crystal Structure Of Transthyretin Variant Y114h gi|253722168 Mass: 12789 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Transthyretin Stability As A Key Factor In Amyloidogenesis gi|259045651 Mass: 13941 Score: 188 Matches: 5(3) Sequences:

5(3) Chain 1, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val 30-->met Variant To 1.7 Angstroms Resolution gi|261824993 Mass: 12738 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Crystal Structure Of Human Transthyretin - Wild Type gi|114318993 Mass: 20300 Score: 188 Matches: 5(3) Sequence

s: 5(3) transthyretin [Homo sapiens] gi|126030594 Mass: 13761 Score: 188 Matches: 5(3) Sequence

s: 5(3) Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin Mascot Search Results Spot 1049

User : JITENDRA VASHIST Email : [email protected] Search title : H:\mass res\LOKESH 31.5.10\TTR2A.wiff (sample number 1) MS data file : C:\DOCUME~1\DRAF40~1.JIT\LOCALS~1\Temp\mas20.tmp Database : NCBInr 20100724 (11505486 sequences; 3925745078 residues) Taxonomy : Homo sapiens (human) (232657 sequences) Timestamp : 27 Jul 2010 at 02:43:37 GMT Protein gi| Chain A, The X-Ray Crystal Structure Refinements Of Normal Human hits 4432 Transthyretin And The Amyloidogenic Val30met Variant To 1.7 : 95 Angstroms Resolution gi| 4354 cytokeratin 9 [Homo sapiens] 76 gi| 7331 keratin 1 [Homo sapiens] 218 gi| 2831 unnamed protein product [Homo sapiens] 7 gi| 1814 epidermal cytokeratin 2 [Homo sapiens] 02

Mascot Score Histogram

Standard scoring MudPIT Ions score or expect cut-off Show sub-sets 0 0 scoring Show pop-ups Suppress pop- Sort unassigned Require bold red Decreasing Score ups

1. gi|443295 Mass: 13810 Score: 262 Matches: 5(5) Sequences: 5(5) emPAI: 2.51 Chain A, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val30met Variant To 1.7 Angstroms Resolution Check to include this hit in error tolerant search

QuerObserve Mr(expt Mr(calc Delt Mis Scor Expec Ran Uniq Peptide y d ) ) a s e t k ue 683.900 1365.78 1365.75 0.03 0.000 610 0 69 1 U R.GSPAINVAVHVFR.K 3 61 17 44 12 697.826 1393.63 1393.61 0.02 622 0 75 3e-05 1 U K.AADDTWEPFASGK.T 8 91 50 41 747.948 1493.88 1493.84 0.03 0.003 663 1 54 1 U R.GSPAINVAVHVFRK.A 1 16 67 49 4 761.873 1521.73 1521.71 0.02 1.9e- 671 1 97 1 U R.KAADDTWEPFASGK.T 1 17 00 17 07 819.402 2455.18 2454.14 1.04 0.000 K.TSESGELHGLTTEEEF 730 0 64 1 U 9 69 38 31 2 VEGIYK.V

Proteins matching the same set of peptides: gi|443297 Mass: 13840 Score: 262 Matches: 5(5) Sequences: 5(5) Chain A, The X-Ray Crystal Structure Refinements Of Normal Human Transthyretin And The Amyloidogenic Val30met Variant To 1.7 Angstroms Resolution gi|1827569 Mass: 13824 Score: 262 Matches: 5(5) Sequences: 5(

5) Chain A, Transthyretin-V122I CARDIOMYOPATHIC MUTANT gi|2098255 Mass: 13806 Score: 262 Matches: 5(5) Sequences: 5(5) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|2098257 Mass: 13886 Score: 262 Matches: 5(5) Sequences: 5(5) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|3891451 Mass: 13711 Score: 262 Matches: 5(5) Sequences: 5(

5) Chain A, Transthyretin (Del Val122) gi|3891560 Mass: 13840 Score: 262 Matches: 5(5) Sequences: 5(5) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|3891562 Mass: 13840 Score: 262 Matches: 5(5) Sequences: 5(5) Chain A, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And Implications For Amyloid Fibril Formation gi|4507725 Mass: 15991 Score: 262 Matches: 5(5) Sequences: 5(

5) transthyretin precursor [Homo sapiens] gi|14719497 Mass: 12671 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, Transthyretin Thr119met Protein Stabilisation gi|17942890 Mass: 13812 Score: 262 Matches: 5(5) Sequences: 5(5

) Chain A, An Engineered Transthyretin Monomer That Is Non-Amyloidogenic - Unless Partially Denatured gi|27065112 Mass: 13807 Score: 262 Matches: 5(5) Sequences: 5(5

) Chain A, Crystal Structure Of The Transthyretin Mutant Ttr Y114c- Data Collected At Room Temperature gi|31615374 Mass: 13718 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, Crystal Structure Of The Transthyretin Mutant Ttr C10aY114C gi|48145933 Mass: 15977 Score: 262 Matches: 5(5) Sequences: 5

(5) TTR [Homo sapiens] gi|50513594 Mass: 13918 Score: 262 Matches: 5(5) Sequences: 5(5

) Chain A, Crystal Structure Of The Transthyretin Mutant A108yL110E Solved In Space Group P21212 gi|55669575 Mass: 12836 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, A Covalent Dimer Of Transthyretin That Affects The Amyloid Pathway gi|62738386 Mass: 13794 Score: 262 Matches: 5(5) Sequences: 5(

5) Chain A, The X-Ray Crystallographic Structure Of The Amyloidogenic Variant Ttr Tyr78phe gi|62738388 Mass: 13791 Score: 262 Matches: 5(5) Sequences: 5(5

) Chain A, Structure Of Ttr R104h: A Non-Amyloidogenic Variant With Protective Clinical Effects gi|73535906 Mass: 13941 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, Crystal Structure Of Human Transthyretin With Bound Iodide gi|114318993 Mass: 20300 Score: 262 Matches: 5(5) Sequences:

5(5) transthyretin [Homo sapiens] gi|114319005 Mass: 15062 Score: 262 Matches: 5(5) Sequences:

5(5) transthyretin [Homo sapiens] gi|119621670 Mass: 15689 Score: 262 Matches: 5(5) Sequences: 5

(5) transthyretin (prealbumin, amyloidosis type I), isoform CRA_b [Homo sapiens] gi|126030508 Mass: 13784 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Transthyretin Mutant I84s At Acidic Ph gi|126030510 Mass: 13768 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Transthyretin Mutant I84a At Low Ph gi|189339646 Mass: 12740 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, Crystal Structure Of The F87mL110M MUTANT OF HUMAN Transthyretin At Ph 4.6. gi|212374952 Mass: 13798 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Transthyretin Variant V20s gi|223674041 Mass: 13456 Score: 262 Matches: 5(5) Sequences: 5

(5) Chain A, Crystal Structure Of Transthyretin In Complex With Iododiflunisal-Betaalaome gi|224510585 Mass: 12996 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of The Apo Form Of Human Wild-Type Transthyretin gi|226438187 Mass: 13784 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Transthyretin Variant Y114h gi|261824993 Mass: 12738 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Human Transthyretin - Wild Type gi|126030594 Mass: 13761 Score: 262 Matches: 5(5) Sequences:

5(5) Chain A, Crystal Structure Of Cys10 Sulfonated Transthyretin