Table 1. Quantification of RC, cytbc1, ATP synthase and terminal cytc oxidases within chromatophores by mass spectrometry.
Chromatophores were co-solubilised with a 15N-labelled artificial protein standard composed of concatenated sequences of tryptic peptides which are known to represent the target proteins in proteomic analysis. This mixture was subjected to trypsin digestion; each digestion time-point was analysed by nanoLC-MS/MS in duplicate. For each proteotypic peptide, the time-point which gave the highest intensity was used for quantification using the ratio between its (14N) monoisotopic ion and the 15N-labelled counterpart at known concentration. Method details are provided in the Methods section and in Supplementary Information. Although some of the peptides had similar quantification results over two or more time-points, only the highest intensity time-point was used in the final dataset. The final numbers for each proteotypic peptide in the Table are the mean of 2 replicates.
| Protein | Tryptic peptide | Quantity (nmol/g total protein) |
Stoichio- metry (ratio per 1 PufM) |
Stoichio- metry (ratio per 24 PufM) |
|---|---|---|---|---|
| RC PufM | AEYQNIFSQVQVR | 724 ± 1 | 1.00 ± 0.00 | 24.0 ± 0.0 |
| RC PufL | ALLSFER | 778 ± 112 | 1.07 ± 0.15 | 25.8 ± 3.7 |
| Cytbc1 FbcC | SLSEPGGPELPEDQVR | 257 ± 3 | 0.36 ± 0.00 | 8.5 ± 0.1 |
| Cytbc1 FbcF | SVQLGQLVDTNAR | 203 ± 14 | 0.28 ± 0.02 | 6.7 ± 0.5 |
| ATP synthase AtpF | LAAAEDQIASAEAGAVR | 65 ± 9 | 0.09 ± 0.01 | 2.1 ± 0.3 |
| ATP synthase AtpX | SDAAAVDAAVAAR | 61 ± 2 | 0.08 ± 0.00 | 2.0 ± 0.1 |
| ATP synthase AtpA | GIQAAEISAILK | 134 ± 6 | 0.18 ± 0.01 | 4.4 ± 0.2 |
| VVDGLGNPIDGK | 143 ± 9 | 0.20 ± 0.01 | 4.8 ± 0.2 | |
| TAIALDTILNQK | 143 ± 1 | 0.20 ± 0.00 | 4.7 ± 0.0 | |
| Cytc oxidase CoxII | VVSEEAYAAWLEQAR | 0 ± 0 | 0.00 ± 0.00 | 0.0 ± 0.0 |
| Cytc oxidase CcoO | AQANPDADTDGLLER | 31 ± 0 | 0.04 ± 0.00 | 1.0 ± 0.0 |