Table 3.
Bias in amino acid identity at the N-terminal (column 1) of the peptide after detected peptides, for unbiased analyses assuming random cleavage. Analysis search for peptides matching translations of the del- (columns 2–4) and swinger-transformed human mitogenome (columns 5–7), and translations of the swinger mitogenomes according to tetra- (columns 8–10) and pentacodons (columns 11–13). Columns 2, 5 , 8 and 11 incicate numbers of detections. ‘Genome’ (columns 3, 6, 9, 12) indicates abundances of that residue in the corresponding hypothetical translations of the complete mitogenome after transformations and non-canonical translations. Biases (columns 4, 7, 10, 13) do not resemble those for carboxyl-extremities of detected peptides (Table 1) and are less extreme. Overall they match random distributions around ‘1’, indicating lack of bias. This suggests that there is no or very little natural proteolysis with cleavage specificity related to the N-terminal of peptides after detected peptides.
| 1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AA | Del |
Swinger |
Swinger |
Swinger |
||||||||
| Tri | Genome | Bias | Tri | Genome | Bias | Tetra | Genome | Bias | Penta | Genome | Bias | |
| A | 8 | 8328 | 1.19 | 6 | 46,838 | 0.79 | 10 | 47,048 | 1.09 | 3 | 46,178 | 0.42 |
| C | 4 | 5680 | 0.87 | 3 | 22,697 | 0.82 | 6 | 22,836 | 1.34 | 8 | 22,108 | 2.31 |
| D | 6 | 4662 | 1.59 | 3 | 21,545 | 0.86 | 7 | 21,752 | 1.64 | 5 | 20,795 | 1.54 |
| E | 6 | 6281 | 1.18 | 8 | 24,954 | 1.98 | 7 | 25,290 | 1.41 | 2 | 24,200 | 0.53 |
| F | 5 | 7868 | 0.79 | 2 | 30,878 | 0.40 | 5 | 30,982 | 0.82 | 2 | 29,626 | 0.43 |
| G | 13 | 12,857 | 1.25 | 8 | 57,120 | 0.87 | 8 | 57,648 | 0.71 | 4 | 55,452 | 0.46 |
| H | 6 | 6578 | 1.13 | 4 | 22,775 | 1.09 | 4 | 22,836 | 0.90 | 2 | 21,803 | 0.59 |
| IL | 20 | 27,890 | 0.89 | 20 | 97,382 | 1.27 | 25 | 97,914 | 1.30 | 18 | 93,464 | 1.23 |
| K | 5 | 8142 | 0.76 | 4 | 30,603 | 0.81 | 5 | 30,982 | 0.82 | 4 | 29,608 | 0.86 |
| M | 5 | 7581 | 0.81 | 6 | 22,553 | 1.64 | 5 | 22,836 | 1.12 | 4 | 21,660 | 1.18 |
| N | 9 | 7723 | 1.44 | 2 | 26,449 | 0.47 | 6 | 26,660 | 1.15 | 3 | 25,427 | 0.75 |
| P | 11 | 12,857 | 1.06 | 5 | 57,489 | 0.54 | 12 | 57,648 | 1.06 | 11 | 55,452 | 1.27 |
| Q | 2 | 5647 | 0.44 | 4 | 24,126 | 1.24 | 4 | 24,206 | 0.84 | 4 | 23,422 | 1.09 |
| R | 3 | 5876 | 0.61 | 8 | 46,786 | 1.06 | 3 | 47,048 | 0.33 | 13 | 45,626 | 1.82 |
| S | 12 | 16,856 | 0.88 | 8 | 68,457 | 0.72 | 19 | 68,800 | 1.41 | 11 | 65,983 | 1.06 |
| T | 11 | 11,954 | 1.14 | 12 | 46,822 | 1.58 | 9 | 47,047 | 0.98 | 8 | 44,813 | 1.14 |
| V | 9 | 11,954 | 0.93 | 13 | 46,591 | 1.72 | 5 | 47,047 | 0.54 | 6 | 44,813 | 0.96 |
| W | 7 | 6838 | 1.27 | 2 | 23,960 | 0.52 | 2 | 24,206 | 0.42 | 2 | 23,118 | 0.55 |
| Y | 6 | 7630 | 0.97 | 2 | 23,238 | 0.53 | 4 | 22,836 | 0.90 | 2 | 21,364 | 0.60 |
| Tot | 148 | 183,202 | 120 | 741,263 | 146 | 745,622 | 112 | 714,912 | ||||