Summary of the Effect of Multiple Reading Frames and Increased Resolution on Detection of Single Nucleotide Substitutions
Detection resolution | |||||
|---|---|---|---|---|---|
| Reading frame | 12 Da | 5 Da | 0.5 Da | ||
| RF1 | 1. (Q) C-A(K) | 1. (Q) C-A (K) | 1. (Q) C-A (K) | ||
| 1. (Q) C-G (E) | 1. (Q) C-G (E) | 3. (Q) A-G (Q) | |||
| 3. (Q) A-G (Q) | 3. (Q) A-G (Q) | 4. (L) C-A (I) | |||
| 3. (Q) A-T (H) | 4. (L) C-A (I) | 4. (L) C-T (L) | |||
| 3. (Q) A-C (H) | 4. (L) C-T (L) | 6. (L) A-G (L) | |||
| 4. (L) C-A (I) | 6. (L) A-G (L) | 6. (L) A-T (L) | |||
| 4. (L) C-T (L) | 6. (L) A-T (L) | 6. (L) A-C (L) | |||
| 6. (L) A-G (L) | 6. (L) A-C (L) | 9. (E) A-G (E) | |||
| 6. (L) A-T (L) | 7. (E) G-C (Q) | 12. (E) G-A (E) | |||
| 6. (L) A-C (L) | 7. (E) G-A (K) | 15. (V) A-G (V) | |||
| 7. (E) G-C (Q) | 9. (E) A-G (E) | 15. (V) A-T (V) | |||
| 7. (E) G-A (K) | 10. (E) G-C (Q) | 15. (V) A-C (V) | |||
| 9. (E) A-G (E) | 10. (E) G-A (K) | 16. (R) A-C (R) | |||
| 10. (E) G-C (Q) | 12. (E) G-A (E) | 18. (R) A-G (R) | |||
| 10. (E) G-A (K) | 15. (V) A-G (V) | 21. (N) C-T (N) | |||
| 12. (E) G-A (E) | 15. (V) A-T (V) | 24. (Y) T-C (Y) | |||
| 15. (V) A-G (V) | 15. (V) A-C (V) | ||||
| 15. (V) A-T (V) | 16. (R) A-C (R) | ||||
| 15. (V) A-C (V) | 18. (R) A-G (R) | ||||
| 16. (R) A-C (R) | 19. (N) A-G (D) | ||||
| 18. (R) A-G (R) | 20. (N) A-T (I) | ||||
| 19. (N) A-G (D) | 21. (N) C-T (N) | ||||
| 20. (N) A-T (I) | 24. (Y) T-C (Y) | ||||
| 21. (N) C-T (N) | |||||
| 24. (Y) T-C (Y) | |||||
| RF1 | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | ||
| 1. (Q) C-G (E)* | 1. (Q) C-G (E)* | 6. (L) A-C (L) | |||
| RF3 | 3. (Q) A-C (H) | 6. (L) A-C (L) | 15. (V) A-C (V) | ||
| 6. (L) A-C (L) | 15. (V) A-G (V) | 21. (N) C-T (N) | |||
| 15. (V) A-G (V) | 15. (V) A-C (V) | 24. (Y) T-C (Y)* | |||
| 15. (V) A-C (V) | 18. (R) A-G (R) | ||||
| 18. (R) A-G (R) | 21. (N) C-T (N) | ||||
| 21. (N) C-T (N) | 24. (Y) T-C (Y)* | ||||
| 24. (Y) T-C (Y)* | |||||
| RF1 | 1. (Q) C-A (K) | 1. (Q) C-A (K) | 1. (Q) C-A (K) | ||
| 1. (Q) C-G (E) | 1. (Q) C-G (E) | 3. (Q) A-G (Q) | |||
| RF4 | 3. (Q) A-G (Q) | 3. (Q) A-G (Q) | 4. (L) C-T (L) | ||
| 3. (Q) A-C (H) | 4. (L) C-T (L) | 16. (R) A-C (R) | |||
| 3. (Q) A-T (H) | 7. (E) G-A (K) | ||||
| 4. (L) C-T (L) | 10. (E) G-C (Q) | ||||
| 7. (E) G-A (K) | 10. (E) G-A (K) | ||||
| 10. (E) G-C (Q) | 16. (R) A-C (R) | ||||
| 10. (E) G-A (K) | 19. (N) A-G (D) | ||||
| 16. (R) A-C (R) | |||||
| 18. (R) A-G (R) | |||||
| 19. (N) A-G (D) | |||||
| RF1 | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | ||
| 1. (Q) C-G (E)* | 1. (Q) C-G (E)* | 24. (Y) T-C (Y)* | |||
| RF6 | 7. (E) G-A (K) | 7. (E) G-A (K) | |||
| 24. (Y) T-C (Y)* | 24. (Y) T-C (Y)* | ||||
| RF1 | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | ||
| 1. (Q) C-G (E) | 1. (Q) C-G (E)* | ||||
| RF3 | 3. (Q) A-C (H)* | ||||
| RF4 | 18. (R) A-G (R) | ||||
| RF1 | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | 1. (Q) C-A (K)* | ||
| RF3 | 1. (Q) C-G (E)* | 1. (Q) C-G (E)* | 24. (Y) T-C (Y)* | ||
| RF6 | 24. (Y) T-C (Y)* | 24. (Y) T-C (Y)* | |||
[i] The 24-nt sequence CAACTAGAAGAGGTAAGAAACTAT was analyzed for all possible single nucleotide substitutions. The output shows the nucleotide position, amino acid and nucleotide change, and detection at three different resolution values
Cases where mutation was not detected because the substitution is in a terminal codon and the other reading frame(s) do not penetrate the codon. Analysis of the same mutations when the 24-nt test sequence was internal to a larger polypeptide showed that they were generally detected.