Table 1.
Mass Spectrometry Data Analysis
| Yeast Species | Aoas (1) | Acr | Safi (1) | Sama | Bai | Cll | Nape |
|---|---|---|---|---|---|---|---|
| Mass spectra | 733,673 | 637,651 | 329,041 | 570,823 | 597,939 | 290,859 | 588,199 |
| PSMs | 246,644 | 411,915 | 332,698 | 298,770 | 223,556 | 125,927 | 263,450 |
| Non-redundant peptides | 31,189 | 41,064 | 43,503 | 49,168 | 33,974 | 34,172 | 41,028 |
| Identified proteins | 2,763 | 3,507 | 3,202 | 3,831 | 3,439 | 3,571 | 3,752 |
| Identified proteins (%) | 35.94 | 52.60 | 51.74 | 61.00 | 54.39 | 60.16 | 66.67 |
| Identified proteins with CUG | 778 | 1,451 | 1,928 | 2,331 | 2,122 | 2,843 | 3,533 |
| Identified proteins with CUG (%) | 33.52 | 46.05 | 49.03 | 56.56 | 47.47 | 56.95 | 66.62 |
| Covered CUG positions | 135 | 449 | 730 | 1,292 | 1,211 | 2,360 | 8,756 |
| PSMs covering CUGs | 1,185 | 2,973 | 3,462 | 5,500 | 4,937 | 5,803 | 51,737 |
| Non-redundant peptides covering CUGs | 210 | 494 | 836 | 1,438 | 1,325 | 2,560 | 10,797 |
| Supported CUG positions | 110 | 361 | 541 | 1,033 | 930 | 1,835 | 7,801 |
| Supported CUG positions (%) | 81.48 | 80.40 | 74.11 | 79.95 | 76.80 | 77.75 | 89.09 |
| Unambiguously translated, supported CUG positions (%)a | 99.09 | 98.89 | 97.78 | 98.74 | 99.03 | 99.24 | 96.45 |
| PSMs with supported CUG = Ser | 418 | 2,038 | 2,192 | 2,984 | 2,635 | 3,031 | 72 |
| PSMs with supported CUG = Leu | 501 | 31 | 36 | 26 | 22 | 14 | 47 |
| PSMs with CUG = Ser at positions also covered by PSMs with CUG = Leu | 357 | 40 | 180 | 102 | 0 | 1 | 2 |
| PSMs with CUG = Leu at positions also covered by PSMs with CUG = Ser | 394 | 18 | 26 | 13 | 0 | 1 | 1 |
| PSMs with supported CUG = Ala | 0 | 3 | 1 | 2 | 5 | 6 | 31,945 |
| PSMs with CUG = Ala at positions also covered by PSMs with CUG = Ser/Leu | 0 | 0 | 0 | 1 | 0 | 1 | 361 |
Aoas (1), A. asiatica sample 1; Acr, A. rubescens; Safi (1), S. fibuligera sample 1; Sama, S. malanga; Bai, B. inositovora; Cll, C. lusitaniae; Nape, N. peltata. See also Data S1 and S2.
a
“Unambiguously translated” refers to all CUG positions for which only peptides with one translation were found. These not only include CUG positions translated by the expected, cognate tRNA-decoded amino acid but also CUG positions translated by other amino acids that might result from genome sequencing ambiguities and differences between sequenced and analyzed strains. For A. asiatica, we regard translation by both serine and leucine cognate tRNACAG as “unambiguous.”