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Table 1 Comparison of in silico fragmentation results for 473 Eawag Orbitrap spectra (formula search)

From: MetFrag relaunched: incorporating strategies beyond in silico fragmentation

  MetFrag2010 MetFrag2.2 CFM-ID MetFrag2.2 + CFM-ID
ChemSpider ChemSpider PubChem PubChem PubChem
Pessimistic ranks
 Median rank 8 4 12 11 8
 Mean rank 74 38 141 127 85
 Mean RRP 0.859 0.894 0.880 0.881 0.901
 Top 1 ranks 73 (15 %) 105 (22 %) 30 (6 %) 43 (9 %) 62 (13 %)
 Top 5 ranks 202 267 145 170 202
 Top 10 ranks 258 320 226 232 276
Expected top ranks
 Top 1 ranks 90 (19 %) 124 (26 %) 43 (9 %) 57 (12 %) 70 (15 %)
 Top 5 ranks 218 280 163 193 213
 Top 10 ranks 274 329 245 261 288
  1. MetFrag2010 and MetFrag2.2 were compared with the same ChemSpider candidate sets; MetFrag2.2 and CFM-ID with the same PubChem candidate sets. Far right: Best top 1 pessimistic ranks obtained by combining MetFrag2.2 and CFM-ID 2.0 with the weights \(\omega _{{\mathrm{Frag}}} = 0.67\) and \(\omega _{\mathrm{CFM}\text {-}\mathrm{ID}} = 0.33\). The expected ranks, which partially account for equally scored candidates as calculated in [16], are shown in the lower part of the table