Skip to main content

Advertisement

Table 4 Results (Top 1, 5 and 10 ranks) using PubChem formula queries on three additional datasets

From: MetFrag relaunched: incorporating strategies beyond in silico fragmentation

Weight term Score Term Weights
\(\omega _{{\mathrm{Frag}}}\) \(S_{C_{{\mathrm{Frag}}}}\) 1 1 1 0 1 0 0
\(\omega _{{\mathrm{RTs}}}\) \(S_{C_{{\mathrm{RT}}}}\) 1 1 0 1 0 1 0
\(\omega _{{\mathrm{Refs}}}\) \(S_{C_{{\mathrm{Refs}}}}\) 1 0 1 1 0 0 1
Dataset Metric Ranks
UF (n = 225) Top 1 ranks 164 (73 %) 9 163 159 3 2 157
UF (n = 225) Top 5 ranks 186 (83 %) 48 189 189 36 13 199
UF (n = 225) Top 10 ranks 191 (53 %) 77 196 192 61 25 204
EQex (n = 289) Top 1 ranks 235 (81 %) 33 232 230 26 11 223
EQex (n = 289) Top 5 ranks 263 (91 %) 87 260 258 88 38 276
EQex (n = 289) Top 10 ranks 270 (93 %) 132 269 263 139 55 280
EQexPlus (n = 310) Top 1 ranks 190 (61 %) 32 183 182 21 8 181
EQexPlus (n = 310) Top 5 ranks 238 (77 %) 84 246 238 83 28 243
EQexPlus (n = 310) Top 10 ranks 254 (82 %) 115 258 247 121 37 256
  1. The weights indicate where ranking parameters were included (1) or excluded (0) from the candidate ranking. Retention time score calculation was performed using the XLOGP3 values of PubChem. \(\omega _{{\mathrm{Refs}}} \cdot S_{C_{{\mathrm{Refs}}}} = \omega _{{\mathrm{Refs}}} \cdot S_{C_{{\mathrm{PNP + PPC}}}}\). See text for explanations