Table 1. Proteins and protein groups identified from normal rat liver plasma membranes and hepatocellular carcinoma Morris hepatoma 7777 plasma membranes using different treatments.
Mass spec data were acquired by a) a QSTAR XL mass spectrometer and b) an Orbitrap Velos mass spectrometer. MS/MS spectra were searched against the Uniprot rat protein database using the Mascot algorithm v.2.3.2 provided with Matrix Science as described in methods. Mascot results were filtered using ProteoIQ software with the following stringent criteria: Mowse score > 28 for all charge states, at least 2 peptides per protein, 1% peptide false discovery rate (FDR) and 1% protein FDR.
| a) QSTAR analysis | |||||
|---|---|---|---|---|---|
| Samples | Total (Proteins) | None | TMD=1 | TMD=2 | TMD>=3 |
| LIPM_Control | 473 | 306 | 86 | 34 | 47 |
| LISW | 625 | 375 | 121 | 44 | 85 |
| LIPD | 375 | 114 | 89 | 34 | 138 |
| MHSW | 603 | 401 | 105 | 37 | 68 |
| MHPD | 355 | 119 | 148 | 40 | 108 |
| Samples | Total (Protein Groups) | None | TMD=1 | TMD=2 | TMD>=3 |
| LIPM_Control | 215 | 142 | 73 | 12 | 17 |
| LISW | 268 | 158 | 110 | 17 | 36 |
| LIPD | 169 | 49 | 120 | 13 | 64 |
| MHSW | 252 | 168 | 84 | 12 | 28 |
| MHPD | 169 | 48 | 121 | 16 | 62 |
| b) Orbitrap analysis | |||||
|---|---|---|---|---|---|
| Samples | Total (Proteins) | None | TMD=1 | TMD=2 | TMD>=3 |
| LISW | 2248 | 1508 | 331 | 103 | 306 |
| LIPD | 955 | 416 | 176 | 82 | 281 |
| MHSW | 2154 | 1544 | 289 | 95 | 226 |
| MHPD | 1036 | 503 | 187 | 83 | 263 |
| Samples | Total (Protein Groups) | None | TMD=1 | TMD=2 | TMD>=3 |
| LISW | 967 | 626 | 175 | 45 | 121 |
| LIPD | 434 | 168 | 102 | 36 | 128 |
| MHSW | 952 | 642 | 161 | 44 | 101 |
| MHPD | 477 | 201 | 110 | 38 | 128 |