Table 1.
Comparison of identification of 2D gel separated spots of rat liver protein by chip-based nanoESI/MS/MS and nanoHPLC-MS/MS
| Spot | Method | Protein | Score | Peptidesmatched | % Cover | ProteinMW (× 10-3) | Decoy Discovery Rate | False Discovery Rate | Accession |
|---|---|---|---|---|---|---|---|---|---|
| 1 | HPLC | Protein disulfide-isomerase | 211 | 7 | 12 | 57.1 | 0 | 0 | gi129729 |
| Multistep | 280 | 15 | 26 | 0 | 0 | ||||
| HPLC | Iodothyronine 5' monodeiodinase | 211 | 7 | 13 | 54.0 | gi202549 | |||
| Multistep | 280 | 15 | 25 | ||||||
| HPLC | Prolyl 4-hydroxylase, beta polypeptide, isoform CRA_a | 211 | 7 | 11 | 59.0 | gi148702818 | |||
| Multistep | 280 | 15 | 25 | ||||||
| HPLC | Prolyl 4-hydroxylase, beta polypeptide, isoform CRA_b | 211 | 7 | 11 | 61.5 | gi148702819 | |||
| Multistep | 280 | 15 | 24 | ||||||
| 2 | HPLC | Methionine adenosyltrans-ferase I, alpha | 304 | 7 | 21 | 43.5 | 0 | 0 | gi19526790 |
| Multistep | 378 | 6 | 28 | 0 | 0 | ||||
| 3 | HPLC | Regucalcin | 230 | 5 | 18 | 33.4 | 0 | 0 | gi6677739 |
| Multistep | 211 | 4 | 14 | 0 | 0 | ||||
| 4 | HPLC | Carbamoyl-phosphate synthetase 1 | 1286 | 28 | 18 | 164.5 | 4 | 17.39 | gi124248512 |
| Multistep | 697 | 23 | 14 | 0 | 0 | ||||
| 5 | HPLC | Carbamoyl-phosphate synthetase 1 | 1221 | 27 | 18 | 164.5 | 3 | 17.65 | gi124248512 |
| Multistep | 1112 | 31 | 20 | 0 | 0 | ||||
| 6 | HPLC | Glutamate de-hydrogenase 1 | 416 | 9 | 17 | 61.3 | 1 | 9.09 | gi6680027 |
| Multistep | 364 | 10 | 17 | 0 | 0 | ||||
| 7 | HPLC | Arginase 1 | 284 | 5 | 16 | 34.8 | 1 | 12.5 | gi7106255 |
| Multistep | 290 | 8 | 26 | 0 | 0 | ||||
| HPLC | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 134 | 4 | 10 | 44.9 | gi584714 | |||
| Multistep | 192 | 6 | 19 | ||||||
| 8 | HPLC | Sorbitol dehydrogenase precursor | 176 | 4 | 11 | 40.7 | 0 | 0 | gi1009706 |
| Multistep | 207 | 6 | 17 | 0 | 0 | ||||
| HPLC | Sorbitol dehydrogenase | 176 | 4 | 12 | 38.2 | gi22128627 | |||
| Multistep | 207 | 6 | 18 | ||||||
| HPLC | L-iditol 2-dehydrogenase | 176 | 4 | 11 | 42.8 | gi397357 | |||
| Multistep | Sorbitol dehydrogenase, isoform CRA_a | 176 | 4 | 14 | 32.0 | gi149023127 | |||
| 9 | HPLC | Fumaryl-acetoacetase | 191 | 4 | 10 | 46.2 | 0 | 0 | gi50973 |
| Multistep | 290 | 6 | 15 | 0 | 0 | ||||
| HPLC | 4-hydroxy-phenyl-pyruvate dioxygenase | 197 | 4 | 10 | 45.1 | gi849053 | |||
| Multistep | F1 protein | 197 | 4 | 10 | 43.6 | gi1841443 | |||
| HPLC | Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase Complexed W/4-(Hydroxymethylphosphinoyl)-3-Oxo-Butanoic Acid | 191 | 4 | 10 | 46.2 | gi13399972 | |||
| Multistep | Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase | 191 | 4 | 10 | 45.9 | gi8569272 | |||
| HPLC | Chain A, Crystal Structure of Fumarylacetoacetate Hydrolase Complexed With Fumarate And Acetoacetate | 191 | 4 | 10 | 46.4 | gi8569274 | |||
| Multistep | Glutamate-ammonia ligase | 187 | 5 | 15 | 42.0 | gi2144563 | |||
| HPLC | Glutamine synthetase | 187 | 5 | 15 | 42.1 | gi31982332 | |||
| Multistep | Long-chain acyl-CoA dehydrog-enase | 122 | 3 | 6 | 48.0 | gi726095 | |||
| 10 | HPLC | Arginase 1 | 232 | 4 | 13 | 34.8 | 0 | 0 | gi7106255 |
| Multistep | 314 | 6 | 23 | 0 | 0 | ||||
| HPLC | Aldo-keto reductase family 1, member D1 | 120 | 3 | 7 | 37.4 | gi20302063 | |||
| Multistep | 69 | 4 | 9 | ||||||
| HPLC | rCG27878 | 120 | 3 | 7 | 37.4 | gi149065268 | |||
| Multistep | 69 | 4 | 9 | ||||||
| 11 | HPLC | Ornithine transcarbamyl-ase, isoform CRA_f | 298 | 5 | 14 | 42.0 | 1 | 14.29 | gi148703731 |
| Multistep | 285 | 7 | 19 | 0 | 0 | ||||
| HPLC | Ornithine transcarbamyl-ase | 297 | 5 | 14 | 39.8 | gi762985 | |||
| Multistep | 284 | 7 | 20 | ||||||
| HPLC | Otc protein | 297 | 5 | 14 | 39.3 | gi19353187 | |||
| Multistep | 284 | 7 | 20 | ||||||
| 12 | HPLC | Alcohol dehydrogenase 1 (class I) | 156 | 3 | 9 | 39.7 | 0 | 0 | gi6724311 |
| Multistep | 102 | 3 | 9 | 0 | 0 | ||||
| HPLC | Alcohol dehydrogenase 1 (class I), isoform CRA_b | 156 | 3 | 11 | 35.3 | gi148680154 | |||
| Multistep | 102 | 3 | 11 | ||||||
| HPLC | Electron transferring flavoprotein, alpha polypeptide | 155 | 3 | 7 | 35.0 | gi13097375 | |||
| Multistep | 429 | 9 | 31 | ||||||
| HPLC | MAWD binding protein homolog 1 | 139 | 5 | 21 | 32.0 | gi31560132 | |||
| 13 | Multistep | Chain A, Methyl-transferase | 284 | 5 | 18 | 32.4 | 1 | 12.5 | gi1942407 |
| HPLC | 236 | 4 | 19 | 0 | 0 | ||||
| Multistep | Glycine N-methyl-transferase | 284 | 5 | 18 | 32.4 | gi6754026 | |||
| HPLC | 236 | 4 | 19 | ||||||
| Multistep | Electron transferring flavoprotein, alpha polypeptide | 121 | 2 | 7 | 35.0 | gi13097375 | |||
| 14 | HPLC | Glutathione S-transferase mu 1 |
193 | 5 | 19 | 26.0 | 1 | 25 | gi6754084 |
| Multistep | 237 | 6 | 24 | 0 | 0 | ||||
| HPLC | mCG131602, isoform CRA_a | 193 | 5 | 17 | 29.1 | gi148669989 | |||
| Multistep | 237 | 5 | 21 | ||||||
| HPLC | mCG131602, isoform CRA_b | 193 | 5 | 19 | 26.6 | gi148669990 | |||
| Multistep | 237 | 5 | 24 | ||||||
| HPLC | mCG131602, isoform CRA_c | 193 | 5 | 19 | 26.7 | gi148669991 | |||
| Multistep | 237 | 5 | 24 | ||||||
| 15 | HPLC | Hemoglobin beta | 378 | 6 | 47 | 15.7 | 0 | 0 | gi229301 |
| Multistep | 403 | 7 | 52 | 0 | 0 | ||||
| HPLC | Hemoglobin, beta adult major chain | 378 | 6 | 47 | 15.7 | gi31982300 | |||
| Multistep | 403 | 7 | 52 | ||||||
| HPLC | Delta-globin | 219 | 4 | 29 | 16.0 | gi122717 | |||
| Multistep | 208 | 5 | 35 | ||||||
| 16 | HPLC | Fatty acid binding protein 1, liver | 149 | 3 | 22 | 14.2 | 0 | 0 | gi8393343 |
| Multistep | 115 | 3 | 22 | 0 | 0 | ||||