Table 1.
Identified proteins ranked by d score
| Spot numbera | Accession number | Protein name | Mass (kDa) | pI | Peptide (coverage)b | Mascot score c | Comparison (CN)d | Abs(d score)e | FDR (%)f | Comparison 2 (HN) | Abs(d score) | FDR (%) | Comparison 3 (CH) | Abs(d score) | FDR (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | Q9UBG3 | cornulin | 53 | 5.73 | 15 (33%) | 143 | (7.8) | 4.0 | - | (3.9) | 4.1 | - | (2.0) | 1.6 | 4.7 |
| 1608 | Q9UL46 | PA28 β | 27 | 5.44 | 8 (40%) | 382 | 3.6 | 3.3 | - | 1.8 | 2.0 | 3.0 | 2.0 | 1.9 | 7.5 |
| 1926 | Q99497 | DJ-1 protein | 20 | 6.33 | 5 (30%) | 83 | 2.1 | 2.7 | - | 1.7 | 2.7 | - | 1.3 | 2.0 | 31 |
| 1094 | P63261 | actin | 40 | 5.55 | 12 (37%) | 317 | 2.5 | 2.8 | - | 1.4 | 1.8 | 3.0 | 1.8 | 1.9 | 7.5 |
| 2234 | P02766 | transthyretin | 13 | 5.57 | 9 (80%) | 361 | (3.0) | 2.8 | - | (2.0) | 2.1 | - | (1.5) | 1.1 | 7.5 |
| 1809 | P04792 | HSPB1 | 22 | 7.83 | 9 (46%) | 289 | (2.8) | 2.7 | - | (1.3) | 1.2 | 12 | (2.2) | 2.0 | 0 |
| 1586 | Q5SRT3 | Cl− intracellular channel 1 | 26 | 4.95 | 7 (29%) | 179 | 2.3 | 2.6 | - | 1.6 | 2.4 | - | 1.4 | 1.1 | 20 |
| 830 | P05787 | Cytokeratin 8 | 53 | 5.52 | 14 (32%) | 141 | 3.6 | 2.4 | - | 3.2 | 2.52 | - | 1.1 | 0.22 | 49 |
| 455 | P02787 | transferrin | 55 | 6.00 | 7 (21%) | 106 | (2.8) | 2.3 | - | (1.3) | 0.77 | 16 | (2.1) | 2.2 | - |
| 2093 | O14558 | Hspβ6 (HSP20) | 16 | 5.95 | 5 (38%) | 162 | (2.8) | 2.3 | - | (1.6) | 1.1 | 9.0 | (1.8) | 1.4 | 5.9 |
| 1306 | O43488 | aflatoxin reductase | 40 | 6.70 | 8 (30%) | 227 | (2.2) | 2.1 | - | (1.6) | 2.02 | - | (1.3) | .76 | 19 |
| 237 | P08123 | α2 type I Collagen | 12 9 |
9.08 | 11 (10%) | 175 | (2.6) | 2.0 | - | (1.0 | 0.080 | 39 | (2.6) | 2.0 | - |
| 1069 | P12277 | Creatine kinase B | 42 | 5.34 | 15 (30%) | 609 | 2.1 | 2.0 | 1.0 | 1.2 | 0.71 | 32 | 1.8 | 1.4 | 16 |
| 870 | P13646 | Cytokeratin 13 | 49 | 4.87 | 19 (34%) | 514 | (4.1) | 1.9 | - | (2.6) | 2.6 | - | (1.6) | 0.61 | 23 |
| 1912 | P09211 | GST π | 23 | 5.43 | 10 (62%) | 125 | (2.1) | 1.6 | - | (1.2) | 0.56 | 20 | (1.7) | 1.4 | 5.9 |
| 1609 | Q06323 | PA28 α | 28 | 5.78 | 14 (54%) | 99 | 2.3 | 1.6 | 2.8 | (1.3) | 0.62 | 32 | 1.8 | 1.0 | 23 |
| 2006 | P04179 | Manganese SOD | 22 | 6.86 | 7 (37%) | 89 | 1.3 | 0.40 | 16 | 2.3 | 3.3 | - | (1.8) | 1.5 | 4.7 |
| 612 | Q5TCJ3 | Lamin A/C | 65 | 6.40 | 19 (30%) | 80 | (1.6) | 1.0 | 5.3 | (2.6) | 2.6 | - | 1.6 | 1.2 | 19 |
| 1141 | P30740 | Serpin B1 (elastase inhibitor) | 42 | 5.90 | 18 (44%) | 402 | (1.2) | 1.3 | 1.9 | (2.1) | 2.4 | - | 1.9 | 0.47 | 45 |
| 1103 | Q8IXI3 | Serpin B2 (SCCA1) | 44 | 6.35 | 16 (52%) | 546 | (1.7) | 0.29 | 16 | (2.0) | 2.2 | - | 1.2 | 1.5 | 16 |
| 1464 | P13645 | Cytokeratin 10 | 59 | 5.09 | 14 (22%) | 122 | (2.1) | 1.3 | 1.9 | (2.1) | 2.1 | - | (1.0) | 0.044 | 49 |
| 753 | P02538 | Cytokeratin 6A | 60 | 7.59 | 18 (31%) | 274 | (1.8) | 0.88 | 6.7 | (2.5) | 1.8 | 1.6 | 1.4 | 0.56 | 43 |
| 801 | P23381 | trp-tRNA synthetase | 53 | 6.03 | 6 (35%) | 235 | 1.7 | 0.97 | 13 | (1.4) | 0.98 | 13 | 2.4 | 2.3 | 7.1 |
Spots were ranked in order of decreasing absolute value of d score as determined by SAM algorithm. Dark grey shading denotes up-regulation in the indicated comparison, light grey shading denotes down-regulation, lack of shading denotes not significant. Spot numbers are as they appear on the master analytical gel. Protein accession numbers are from the SwissProt database. Predicted protein masses and isoelectric points are based on conceptual translation. CN: comparison of cancer and normal. HN: comparison of HSIL and normal. CH: comparison of cancer and HSIL.
Number of peptides that matched the identified protein sequence, followed by percent sequence coverage.
Mascot score based on combined peptide mass fingerprinting and masses of collisionally-induced dissociation peptides
Fold change in expression. Values in parentheses are decreases, other values are increases.
Absolute value of d(i) from SAM calculation.
False discovery rate from SAM calculation.