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Table 1 Comparison of identification of 2D gel separated spots of rat liver protein by chip-based nanoESI/MS/MS and nanoHPLC-MS/MS

From: Multi-Segment Direct Inject nano-ESI-LTQ-FT-ICR-MS/MS For Protein Identification

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