Matching Experimental Spectra against a Database of ≈120,000 Yeast Peptides with k = 1 andk = 2 Mutations
| No. | Peptide | Spectral quality, p | Rank in bound-and-branch algorithm | Rank in spectral alignment | |||||
| Mutations | Modifications | Modifications | |||||||
| k = 1 | k = 2 | k = 1 | k = 2 | k = 1 | k = 2 | ||||
| 1 | KYNLSDQMDFVK | 0.58 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 2 | LSDFLHVSSGSDEK | 0.57 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 3 | EVTAALENAAVGLVAGGK | 0.56 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 4 | SPPVYSDISR | 0.55 | 1 | 3 | 1 | >500 | 3 | >500 | |
| 5 | TGLSALMSK | 0.50 | 1 | 1 | 1 | 2 | 1 | 1 | |
| 6 | MFHVDVAR | 0.50 | 1 | 1 | 1 | 190 | 1 | >500 | |
| 7 | ATIDILHAK | 0.44 | 1 | 1 | 1 | 1 | 1 | 2 | |
| 8 | HEHYLAYK | 0.44 | 1 | 1 | 1 | 230 | 1 | 16 | |
| 9 | YVQNLANLATFFR | 0.42 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 10 | NQFDFVEGEISK | 0.42 | 1 | 1 | 1 | 1 | 1 | 2 | |
| 11 | LDGIYVGIAPLVGK | 0.39 | 1 | 1 | 1 | 1 | 1 | 4 | |
| 12 | LGLAPEGSK | 0.39 | 1 | 1 | 1 | 8 | 7 | 5 | |
| 13 | LGWSLSFDA | 0.39 | 1 | 1 | 1 | 1 | 1 | 3 | |
| 14 | AALQTYLPK | 0.39 | 1 | 3 | 1 | 3 | 1 | 1 | |
| 15 | YLPDASSQVK | 0.38 | 1 | 1 | 1 | 3 | 1 | 14 | |
| 16 | DTENGGEATFGGIDESK | 0.38 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 17 | IDSVSQLQNVAETTK | 0.37 | 1 | 1 | 1 | 1 | 1 | 69 | |
| 18 | VLGAEEFPVQGEVVK | 0.37 | 1 | 1 | 1 | 1 | 1 | 23 | |
| 19 | DTSHGEITLSAPYK | 0.36 | 1 | 1 | 1 | 1 | 1 | 13 | |
| 20 | LEGVYSEIYK | 0.35 | 1 | 3 | 2 | 3 | 1 | 1 | |
| 21 | IAYEIELGDGIPK | 0.35 | 1 | 1 | 2 | 1 | 1 | 1 | |
| 22 | GAPEIDVLEGETDTK | 0.33 | 1 | 1 | 1 | 1 | 1 | 3 | |
| 23 | GDLTSPDDMENAINESK | 0.32 | 1 | 1 | 1 | 4 | 1 | 3 | |
| 24 | QDFAEATSEPGLTFAFGK | 0.31 | 1 | 2 | 1 | 1 | 1 | 1 | |
| 25 | LFGDLNASNIDDDQR | 0.30 | 1 | 2 | 1 | 5 | 1 | 125 | |
| 26 | DVDLIESMKDDIMR | 0.29 | 1 | 2 | 1 | 17 | 1 | 20 | |
| 27 | LIPFLEYLATQQTK | 0.29 | 2 | 13 | 3 | 6 | 7 | 284 | |
| 28 | LPNSNVNIEFATR | 0.27 | 1 | 2 | 2 | 35 | 9 | 14 | |
| 29 | LFKPFLDPVTVSK | 0.27 | 1 | 14 | 2 | 18 | 8 | 10 | |
| 30 | SPSALELQVHEIQGK | 0.27 | 1 | 1 | 1 | 1 | 1 | 20 | |
| 31 | FYIINAPFGFSTAFR | 0.27 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 32 | TAPVSSTAGPQTASTSK | 0.26 | 1 | 1 | 1 | 1 | 1 | 1 | |
| 33 | AHNGDLVNAIMSLSK | 0.23 | 2 | 3 | 2 | 1 | 23 | 256 | |
| 34 | GSASGDLTFLASDSGEHK | 0.22 | 1 | 2 | 1 | 1 | 1 | 124 | |
| 35 | DNQIYAIEKPEVFR | 0.21 | 1 | 22 | 1 | >500 | 29 | 445 | |
| 36 | KPENAETPSQTSQEATQ | 0.15 | 3 | >500 | 8 | >500 | 286 | >500 | |
[i] Matching is done by three methods: Mutation-tolerant branch-and-bound algorithm; modification-tolerant branch-and-bound algorithm; and modification-tolerant spectral alignment algorithm. The table shows the ranks of the correct hits in the ranked list of top-scoring hits (rank 1 corresponds to correct peptide identification).