Table 3.
Proteins were identified and quantified with ProQuant. 68 proteins that were found to be common in at least two separate sets of samples and identified with >99% confidence (corresponding to a protein score cut off >2.0) were clustered using K-means cluster analysis software. K was set to four and ProQuant ratios are shown with the corresponding 95% CI. The iTRAQ ratios were also determined by Spectrum Mill for comparison. The complete set of results is included in the Supplementary material.
| Protein ID | Database Accession # | Pro Quant Results | Spectrum Mill Results | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| # pept | Score | day4:day0 (95% CI) | day8:day0 (95% CI) | day12:day0 (95% CI) | # pept | Score | day4: day0 | day8: day0 | day12: day0 | ||
| Cluster 1 Proteins | |||||||||||
| haptoglobin | gi|8850219 | 13 | 20.6 | 6.5 (2.4;18) | 56 (25;127) | 25 (2.3;273) | 16 | 249 | 6.7 | 46 | 36 |
| serum amyloid A | gij200904 | 1 | 22 | 4.7 | 21 | 2.3 | 1 | 15 | 8.5 | 24 | 5.8 |
| Cluster 2 Proteins | |||||||||||
| alpha 1 microglobulin/bikunin | gi|6680684 | 3 | 6.0 | 2.5 (2.0;3.2) | 4.3 (3.0; 6.1) | 5.5 (3.6;8.4) | 3 | 46.8 | 2.3 | 4 | 5.4 |
| coagulation factor XII (Hageman factor) | gi|37046881 | 2 | 3.7 | 2.8 (0;11044) | 5.2 (−) | 3.7 (0;2449642) | 2 | 31.6 | 2.7 | 2.8 | 4.5 |
| gamma-actin | gi|809561 | 7 | 11.6 | 2.1 (1.6;2.8) | 2.8 (2.1;3.8) | 8.8 (7.3;11) | 6 | 86.3 | 2.7 | 4.9 | 12 |
| heat shock protein 1, alpha | gi|6754254 | 2 | 2.9 | 1.6 (0.66;4.0) | 3.7 (2.3;6.1) | 14 (6.5;30) | 3 | 40.2 | 1.6 | 4.8 | 13 |
| hemopexin | gi|23956086 | 25 | 45.9 | 2.7 (2.5;2.9) | 4.0 (3.6;4.4) | 4.8 (4.2;5.4) | 32 | 510 | 3.1 | 5.4 | 7.4 |
| inter alpha-trypsin inhibitor, heavy chain 4 | gi|9055252 | 21 | 39.7 | 2.9 (2.1;4.2) | 5.6 (3.9;8.1) | 4.3 (3.0;6.0) | 28 | 416 | 3 | 6.6 | 4 |
| inter-alpha trypsin inhibitor, heavy chain 3 | gi|6680496 | 10 | 18.1 | 2.7 (2.2;3.3) | 4.7 (3.9;5.6) | 5.9 (4.7;7.4) | 13 | 221 | 3.4 | 5.4 | 6 |
| Ldh1 protein | gi|62740223 | 4 | 5.0 | 4.0 (1.5;10.8) | 7.8 (5.5;11) | 15 (9.6;22) | 7 | 87.2 | 10 | 12 | 24 |
| leucine-rich alpha-2-glycoprotein | gi|16418335 | 3 | 6.0 | 3.1 (2.3;4.3) | 3.7 (2.4;5.6) | 4.1 (2.7;6.3) | 4 | 54.8 | 3.1 | 5.6 | 5.9 |
| proteasome (prosome, macropain) subunit, alpha type 1 | gi|33563282 | 2 | 2.3 | 3.2 (2.0;5.0) | 3.6 (2.0;6.6) | 8.1 (6.3;10) | 2 | 27.8 | 3.5 | 4.6 | 8.1 |
| quiescin Q6 | gi|49904664 | 5 | 8.6 | 1.9 (1.5;2.5) | 2.7 (2.2;3.3) | 3.7 (2.9;4.7) | 5 | 73.5 | 2.3 | 3 | 3.9 |
| serum amyloid P-component (SAP) | gi|297547 | 7 | 10.6 | 4.1 (3.3;5.0) | 8.2 (6.8;10) | 15 (11;20) | 7 | 111 | 5.5 | 12 | 24 |
| serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10 | gi|31981720 | 5 | 10.0 | 2.2 (1.8;2.6) | 3.8 (2.7;5.1) | 4.8 (3.1;7.2) | 8 | 116 | 2.2 | 4.5 | 6.3 |
| Cluster 3 Proteins | |||||||||||
| alpha-2-HS-glycoprotein/fetuin | gi|7304875 | 7 | 11.5 | 1.4 (1.0;1.8) | 1.2 (0.71;1.9) | 2.1 (1.0;4.0) | 9 | 149 | 1.8 | 2 | 4 |
| angiotensinogen precursor | gi|2842775 | 6 | 6.7 | 1.5 (1.1;2.0) | 0.89 (0.69;1.2) | 2.0 (1.5;2.6) | 4 | 60.1 | 1.4 | 1.4 | 2.3 |
| apolipoprotein H; beta-2-glycoprotein I | gi|2765102 | 4 | 6.2 | 1.9 (1.6;2.3) | 1.3 (0.70;2.3) | 1.6 (1.1;2.4) | 6 | 79.9 | 2.4 | 2.4 | 2.6 |
| carbonic anhydrase 1 | gi|15029975 | 2 | 4.0 | 3.4 (2.5;4.5) | 4.0 (2.9;5.3) | 0.65 (0.28;1.5) | 2 | 34.4 | 4.5 | 5.5 | 1 |
| carbonic anhydrase 2 | gi|33243954 | 8 | 12.7 | 3.2 (2.2;4.8) | 3.6 (2.8;4.6) | 0.85 (0.54;1.3) | 7 | 98.5 | 4.3 | 5 | 1.6 |
| ceruloplasmin | gi|38614350 | 24 | 41.7 | 1.8 (1.7;2.0) | 2.0 (1.8;2.2) | 3.7 (3.4:4.1) | 32 | 500 | 1.9 | 2.5 | 3.7 |
| clusterin/apolipoprotein J; apoJ | gi|49523333 | 10 | 20.3 | 2.1 (1.8;2.5) | 2.0 (1.6;2.6) | 2.0 (1.5;2.8) | 12 | 179 | 2.1 | 3.1 | 3.2 |
| complement component 3 | gi|23956044 | 67 | 120 | 1.6 (1.4;1.8) | 2.3 (2.0;2.6) | 2.7 (2.3;3.1) | 82 | 1207 | 2.3 | 3.2 | 4.1 |
| complement component 4 (within H-2S) | gi|6753226 | 26 | 53.2 | 2.7 (2.4;2.9) | 1.7 (1.4;2.1) | 1.9 (1.5;2.3) | 32 | 456 | 2.9 | 2.3 | 4.3 |
| complement component factor i | gi|6671744 | 5 | 6.0 | 1.7 (1.3;2.2) | 1.2 (0.69;2.2) | 1.6 (0.65;4.0) | 4 | 61.6 | 1.9 | 2.2 | 2.4 |
| epidermal growth factor receptor isoform 1 | gi|46560582 | 6 | 12.0 | 1.3 (1.1;1.6) | 1.5 (1.3;1.6) | 1.2 (0.85;1.6) | 7 | 114 | 1.5 | 1.7 | 1.5 |
| fetub protein | gi|17390796 | 2 | 2.8 | 1.5 (1.2;1.9) | 1.4 (1.3;1.6) | 2.0 (1.2;3.4) | 2 | 30.4 | 2.2 | 2.1 | 2.4 |
| fibrinogen, B beta polypeptide | gi|33859809 | 14 | 25.8 | 1.3 (1.1;1.5) | 2.6 (2.0;3.4) | 1.5 (1.1;1.9) | 17 | 270 | 1.8 | 4.9 | 2.6 |
| fibrinogen, gamma polypeptide | gi|19527078 | 12 | 21.6 | 1.4 (1.2;1.7) | 2.5 (2.0;3.1) | 1.6 (1.2;2.1) | 17 | 262 | 1.8 | 3.9 | 3 |
| hemolytic complement | gi|6754164 | 11 | 13.3 | 1.4 (1.1;1.8) | 2.0 (1.5;2.8) | 1.6 (1.2;2.0) | 12 | 160 | 1.8 | 1.9 | 1.6 |
| histidine-rich glycoprotein Hrg | gi|37548631 | 2 | 4.0 | 1.4 (1.1;1.8) | 1.4 (1.0;1.9) | 1.5 (1.0;2.1) | 4 | 62.5 | 1.7 | 2 | 2.1 |
| histocompatibility 2, complement component | |||||||||||
| factor B | gi|6996919 | 6 | 11.6 | 1.6 (1.3;1.9) | 3.0 (1.8;5.0) | 2.3 (1.5;3.5) | 6 | 96.9 | 2.2 | 5.1 | 5 |
| inter-alpha trypsin inhibitor, heavy chain 2 | gi|6754384 | 4 | 6.4 | 1.7 (1.2;2.5) | 1.1 (0.71;1.7) | 1.5 (0.96;2.4) | 6 | 81.9 | 1.9 | 1.5 | 1.8 |
| kininogen 1 | gi|12963497 | 13 | 21.3 | 1.5 (1.3;1.7) | 2.0 (1.5;2.7) | 2.1 (1.6;2.8) | 17 | 225 | 2 | 3 | 3.4 |
| orosomucoid 1 | gi|15215270 | 6 | 10.5 | 2.3 (1.9;2.8) | 2.3 (1.7;3.2) | 3.2 (2.0;5.1) | 7 | 96.9 | 3.1 | 7.6 | 13 |
| serine (or cysteine) proteinase inhibitor, clade D, member 1 | gi|21961582 | 5 | 9.4 | 1.3 (1.1;1.6) | 1.3 (1.1;1.5) | 1.6 (1.3;1.8) | 6 | 91.7 | 1.5 | 1.6 | 1.8 |
| serine (or cysteine) proteinase inhibitor, clade G, member 1 | gi|6753218 | 10 | 20.5 | 1.6 (1.4;1.9) | 1.7 (1.4;2.0) | 2.5 (2.0;3.2) | 14 | 206 | 2 | 2.4 | 3.6 |
| TAGL-delta | gi|33340158 | 2 | 3.3 | 1.6 (0.86;3.1) | 1.3 (0.55;3.0) | 2.2 (1.4;3.7) | 1 | 13.4 | 1.4 | 0.9 | 1.8 |
| transferrin | gi|20330802 | 39 | 84.1 | 1.4 (1.3;1.4) | 1.5 (1.4;1.7) | 2.4 (2.2;2.7) | 52 | 827 | 1.6 | 2 | 3.7 |
| vitamin D-binding protein | gi|193446 | 10 | 18.5 | 1.9 (1.6;2.2) | 1.2 (1.0;1.4) | 1.4 (1.1;1.7) | 12 | 188 | 2.1 | 1.5 | 1.6 |
| Cluster 4 Proteins | |||||||||||
| adiponectin, C1Q and collagen domain containing | gi|20381159 | 4 | 2.9 | 2.6 (1.4;4.7) | 1.5 (0.83;2.6) | 0.72 (0.29;1.8) | 2 | 33.3 | 2.5 | 1.4 | 0.8 |
| Afm protein | gi|20072386 | 4 | 7.4 | 1.0 (0.75;1.3) | 0.75 (0.49;1.2) | 1.0 (0.65;1.6) | 5 | 75.1 | 1 | 0.8 | 1.1 |
| alpha-2 macroglobulin MUG1 - mouse | gi|109550 | 19 | 29.2 | 0.88 (0.78;1.0) | 0.56 (0.49;0.63) | 0.53 (0.47;0.60) | 23 | 298 | 1.1 | 0.6 | 0.6 |
| apolipoprotein A-I | gi|6753096 | 10 | 23.2 | 1.1 (1.0;1.2) | 1.2 (1.0;1.4) | 0.55 (0.43;0.70) | 21 | 300 | 1.4 | 1.3 | 1 |
| apolipoprotein A-IV | gi|14789706 | 11 | 20.1 | 0.88 (0.73;1.1) | 0.48 (0.33;0.70) | 0.50 (0.29;0.86) | 13 | 188 | 1.2 | 1.6 | 2.6 |
| apolipoprotein D | gi|75677437 | 3 | 4.5 | 4.2 (3.3;5.3) | 1.0 (0.75;1.3) | 0.8 (0.7;0.9) | 3 | 45.8 | 4.4 | 1.5 | 0.9 |
| apolipoprotein E | gi|6753102 | 7 | 9.6 | 1.4 (1.1;1.7) | 0.63 (0.38;1.0) | 1.1 (0.65;1.9) | 6 | 87.4 | 1.5 | 1.2 | 1.7 |
| carboxypeptidase N, polypeptide 1 | gi|15928421 | 3 | 2.5 | 1.5 (1.0;2.3) | 1.0 (0.51;2.0) | 1.1 (0.47;2.6) | 2 | 30.3 | 2.1 | 1.5 | 1.6 |
| carboxypeptidase N, polypeptide 2 homolog | gi|59958377 | 7 | 8.3 | 1.3 (1.2;1.5) | 1.1 (0.90;1.3) | 1.2 (1.0;1.5) | 10 | 134 | 1.4 | 1.3 | 1.4 |
| complement component 8, beta subunit | gi|33563297 | 2 | 4.0 | 1.2 (0.83;1.8) | 1.0 (0.3;4.0) | 0.88 (0.21;3.6) | 1 | 19 | 1 | 1.1 | 1 |
| complement component 9 | gi|15375312 | 4 | 8.0 | 2.0 (1.7;2.4) | 1.3 (1.0;1.5) | 1.0 (0.74;1.2) | 6 | 102 | 2.1 | 1.4 | 1 |
| complement component C1SA | gi|27462724 | 2 | 3.7 | 0.7 (−) | 0.60 (−) | 1.0 (−) | 3 | 47.8 | 2 | 2.6 | 2.8 |
| contraspin | gi|54173 | 16 | 40.0 | 1.2 (1.1;1.3) | 0.79 (0.66;0.94) | 0.72 (0.61;0.86) | 20 | 361 | 1.9 | 1.8 | 1.9 |
| Es1 protein | gi|22135640 | 14 | 29.4 | 0.66 (0.61;0.72) | 0.48 (0.42;0.54) | 0.52 (0.43;0.63) | 19 | 301 | 0.9 | 0.7 | 0.9 |
| fibrinogen, alpha polypeptide | gi|33563252 | 13 | 23.2 | 1.2 (1.0;1.4) | 1.4 (1.2;1.63) | 1.0 (0.88;1.2) | 19 | 261 | 1.6 | 4.1 | 1.9 |
| glycosylphosphatidylinositol specific phospholipase D1 | gi|6680069 | 5 | 5.1 | 1.1 (0.93;1.4) | 0.6 (0.42;0.86) | 1.3 (1.2;1.5) | 3 | 44.9 | 1.1 | 0.6 | 1.2 |
| Gsn protein | gi|38014369 | 8 | 10.1 | 1.6 (1.5;1.8) | 1.1 (1.0;1.4) | 0.99 (0.81;1.2) | 11 | 152 | 1.6 | 1.2 | 1 |
| H-2 class I histocompatibility antigen, Q10 alpha chain precursor | gi|122120 | 10 | 17.8 | 1.4 (1.2;1.6) | 1.0 (0.87;1.2) | 0.65 (0.42;1.0) | 9 | 139 | 1.7 | 1.3 | 1 |
| LIFr protein (leukemia inhibitory factor receptor) | gi|21594125 | 3 | 5.5 | 1.6 (0.75;3.3) | 1.0 (0.25;4.2) | 0.47 (0.09;2.4) | 4 | 50.4 | 2.2 | 1 | 0.5 |
| mannose binding lectin, serum (C) | gi|6754656 | 4 | 6.3 | 1.4 (1.1;1.8) | 0.94 (0.7;1.2) | 0.79 (0.45;1.4) | 5 | 71 | 2 | 1.4 | 1.4 |
| paraoxonase 1 | gi|7242183 | 5 | 7.9 | 1.2 (0.85;1.7) | 0.42 (0.31;0.58) | 0.37 (0.19;0.74) | 5 | 73.6 | 1.4 | 0.7 | 0.9 |
| plasminogen | gi|31982113 | 7 | 7.6 | 1.0 (0.85;1.3) | 1.1 (0.98;1.3) | 1.2 (1.0;1.5) | 11 | 140 | 1.8 | 2 | 1.8 |
| pregnancy zone protein | gi|34785996 | 43 | 90.1 | 1.2 (1.1;1.2) | 1.3 (1.2;1.4) | 0.92 (0.84;1.0) | 55 | 864 | 1.3 | 1.7 | 1.3 |
| serine (or cysteine) proteinase inhibitor, clade A, member 6 | gi|6680856 | 4 | 6.5 | 1.2 (0.88;1.5) | 1.0 (0.78;1.3) | 0.46 (0.32;0.67) | 3 | 45.9 | 1.5 | 1.1 | 0.6 |
| serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1 | gi|18252782 | 12 | 23.5 | 1.2 (0.85; 1.6) | 1.0 (1.5;1.8) | 1.2 (0.73;1.9) | 13 | 198 | 1.6 | 2.6 | 3.2 |
| serine (or cysteine) proteinase inhibitor, clade F, member 2 | gi|6679383 | 6 | 9.7 | 1.2 (0.87;1.6) | 1.5 (1.0;2.3) | 1.0 (0.7;1.5) | 6 | 95.3 | 1.4 | 1.9 | 1.6 |
| serpina1c protein | gi|15929675 | 15 | 31.9 | 1.0 (0.80;1.3) | 1.0 (0.81;1.3) | 0.67 (0.43;1.1) | 22 | 375 | 1.7 | 1.6 | 1.5 |
| vitronectin | gi|15215172 | 4 | 4.2 | 1.1 (0.65;1.9) | 1.0 (0.41;2.6) | 0.84 (0.42;1.7) | 4 | 57.6 | 2.1 | 2 | 2 |
| zinc-alpha-2-glycoprotein 1 | gi|29838430 | 6 | 8.6 | 1.3 (1.0;1.6) | 0.59 (0.34;1.0) | 0.83 (0.43;1.6) | 5 | 69.9 | 1.6 | 1.6 | 3.1 |