Table I. Hash identifiers to access raw mass spectrometry files for each MudPIT run.
Individual runs are organized by cell fraction, extraction, and protease to generate peptides for analysis. MM, microsomal membrane.
| Cell fraction | Extraction/digestion | Sample name used in supplemental Tables S1–S5 | At https://www.proteomecommons.org/tranche/downloads.jsp, the raw mass spectrometry files can be downloaded using the following hash identifiers. In all cases, there are two files ranging from 100 MB to 1.5 GB that are archived and compressed tar.gz files: use tar −xzf Linux command to uncompress to *.RAW files (1 per MudPIT step) |
|---|---|---|---|
| PBMC NEs | NaOH/CNBr-trypsin | HsNaOH-NE_NT_lymphocytes_CNBrTi_1 | 4mWjs+LvJQb4FUwQD8O3X5MkkLit6/3bHJfJZK3owfOX4jwMtCUQFhRv95ORUTT8gT5HKx6RdVxGlCjy/nOHw/pjLeMAAAAAAAAGUg== |
| PBMC NEs | NaOH/trypsin | HsNaOH-NE_NT_lymphocytes_Ti_1 | 5aTYg17TJJuGrxJ/wra09yMtKGoVwtlgYWi+EK7Np92HD73ed5417f2/x0ndBFzSjLxwFldZheB74gYe829QI8CDDiwAAAAAAAAFrQ== |
| PBMC NEs | NaOH/proteinase K | HsNaOH-NE_NT_lymphocytes_PK_1 | MBcaJI2EOh07R/EEOLUVt85OXiVbebs7/PiRkN3HvoazDKMmEZxw53RLG96Vx9pgGhIxM0Dxk2O05V0QiEiQi0+oUqoAAAAAAAAGlQ== |
| PBMC NEs | Salt-detergent/trypsin | HsSD-NE_NT_lymphocytes_Ti_1 | rgMMQvG4dw8tJ9WeX0DHi0k6vvEclU34F8mzsnExggk9AbENEtfaBPxvTuBlhJ/iAnDU7XQLLNr8fJV2W72mziU6KrMAAAAAAAAFsQ== |
| PBMC NEs | Salt-detergent/proteinase K | HsSD-NE_NT_lymphocytes_PK_1 | bQnUrYCBdxRh8wM32qka9Jg80U4ow7Z0HK+SmdbPbxPVo3TzLgeTqCWgzKPDYAkUltDGXybehz2ZFVq2EJ+G/et3AiwAAAAAAAAGmQ== |
| PHA-treated PBMC NEs | NaOH/CNBr-trypsin | HsNaOH-NE_PHA_lymphocytes_CNBrTi_1 | /0iTLp3cH9L60CR441Dxg/REq/GKoYRz9Kd/QloEd+3h265EsD1S213sb8ic267lWS5gGDdQHV3xR+T7qZ36K4+O/ZUAAAAAAAAGXA== |
| PHA-treated PBMC NEs | NaOH/trypsin | HsNaOH-NE_PHA_lymphocytes_Ti_1 | gKqv8i+5tPSdMhZM9IZW93nSIXTeQUpYhgyc6SEXUgYJAj+AqeF49+VneqJ5RTQQrEnOM9t2ANPZQJWRZAJaKY0uMBAAAAAAAAAFtQ== |
| PHA-treated PBMC NEs | NaOH/proteinase K | HsNaOH-NE_PHA_lymphocytes_PK_1 | pi3VbyTD3uo8WvUrRgmJn0phN7KpMp5yNInoWpvXSInLu/N0cNKjTY79b3okjGy6+e5zSkQATmN2dQzQ4giyJMdVmvMAAAAAAAAGnw== |
| PHA-treated PBMC NEs | Salt-detergent/trypsin | HsSD-NE_PHA_lymphocytes_Ti_1 | 5nw33XkNPBMdAuQNg6HRD2MPyTa7osxDObK2cxSdAWtVHsRV+sC3kW6omUK3PrvBNa4WCarVz3Hnskjrbn4e7JuU6+sAAAAAAAAFuw== |
| PHA-treated PBMC NEs | Salt-detergent/proteinase K | HsSD-NE_PHA_lymphocytes_PK_1 | QPGdJRqWff6OE9isf9e9zSnB9D0xmV0rQzyR7+Jy5Z6hZZNQDzuGYKNO5+vZJFLxasQ7/Tx4lWHp/Jd5yztAJ095NuUAAAAAAAAGpA== |
| Liver MMs | NaOH/CNBr-trypsin | MmNaOH-MM_liver_CNBrTi_1 | Y+ITtCT8NMlD0geT1lJiVcUIdaOHJmM08umEd9yhyGOq/rqjAkuft0Txw1yeznfC8iXNbkfR/0v35Y0qLBhVyvrgaSwAAAAAAAAGBg== |
| Liver MMs | NaOH/CNBr-trypsin | MmNaOH-MM_liver_CNBrTi_2 | 2KBwq4C/GrCKjyrUMRoRdZ55hzMbJr3wc+O3kZqwnFLV/90uaYuK64FxNneldmnQ7HO1dRNBaNG51EGUnz3EV18OrusAAAAAAAAGAA== |
| Liver MMs | NaOH/trypsin | RnNaOH-MM_liver_Ti_1 | bpp6s9dcwf3lzclX0cPDJCJ01f97QesmXl6anF4PVaUNuNmfdIRrtqkELKcBM6l2X08B/d69Hys6o4vUq66TYHBc4CQAAAAAAAAFaQ== |
| Liver MMs | NaOH/trypsin | RnNaOH-MM_liver_Ti_2 | 7wO8Wz/6iv2rZU5WACjlm1sY5sIkiMWTC5X2+Tjyt5SN+fPoCR/LxuWiD3DetTh+oTWNkU7wd6gp2c3XKx8Oybxl6HMAAAAAAAAFaQ== |
| Liver MMs | NaOH/trypsin | RnNaOH-MM_liver_Ti_3 | ElAxLpoQLOHTnIp0FpP1FeRrEckCbdz0VHUt4h9ISX8v8sMEoutFOarYhBK3+d+jUv1Ihe5rRfXhhR7UcXqx0Bicw4sAAAAAAAAFaQ== |
| Liver MMs | NaOH/trypsin | RnNaOH-MM_liver_Ti_4 | cnJ7dLVqF73eGbFqgZyTn3Egb/XL2RzMWrP7gXG41VfvbRri1eHa1uaHWjvMjbXGdvpq4XCQoz1u+gU//rR/MO7/hckAAAAAAAAFaQ== |
| Liver MMs | NaOH/proteinase K | RnNaOH-MM_liver_PK_1 | ENorMHs0SFhkyD9Y5w4gbEh2bVCdl7gT5SF6dnp0zebaxoFG7kYpPTwYFQXGmhPBjKR/ZG8ewsnnSZZcEzmJZvYq8ecAAAAAAAAGVA== |
| Liver MMs | NaOH/proteinase K | RnNaOH-MM_liver_PK_2 | H36mWYfElnzq6ISRTgc6v6VJVs4WxrUkCNa0LTmufeP+OoMPQaxkkBxn6nHlEv8iCgcw8ghryUbgIY9i+Udjk4k8XnsAAAAAAAAGUg== |