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Table 3 PubChem and ChemSpider results for 473 Eawag orbitrap spectra with formula retrieval, including in silico fragmentation, RT and reference information as shown, with the given \(\omega _i\) for the highest number of Top 1 ranks

From: MetFrag relaunched: incorporating strategies beyond in silico fragmentation

  MetFrag2.2 MetFrag2.2 + CFM-ID
Database ChemSpider PubChem PubChem PubChem
RT/log P Model CDK XlogP CDK XlogP XLOGP3 CDK XlogP
\(\omega _{{\mathrm{Frag}}}\) (\(S_{C_{{\mathrm{Frag}}}}\)) 0.49 0.57 0.50 0.33
\(\omega _{{\mathrm{RT}}}\) (\(S_{C_{{\mathrm{RT}}}}\)) 0.19 0.02 0.16 0.03
\(\omega _{{\mathrm{Refs}}}\) (\(S_{C_{{\mathrm{Refs}}}}\)) 0.32 0.41 0.34 0.35
\(\omega _{{\mathrm{CFMID}}}\) (\(S_{C_{{\mathrm{CFMID}}}}\)) 0.29
Median rank 1 1 1 1
Mean rank 6.5 35 41 18
Mean RRP 0.990 0.977 0.977 0.978
Top 1 ranks 420 (89 %) 336 (71 %) 336 (71 %) 343 (73 %)
Top 5 ranks 447 396 398 411
Top 10 ranks 454 422 414 429
  1. For PubChem \(\omega _{{\mathrm{Refs}}} \cdot S_{C_{{\mathrm{Refs}}}} = \omega _{{\mathrm{Refs}}} \cdot (S_{C_{{\mathrm{PNP + PPC}}}})\); for ChemSpider \(S_{C_{{\mathrm{Refs}}}} = S_{C_{{\mathrm{CRC}}}}\) only. See text for explanations. Far right: combining CFM-ID results to incorporate complementary fragmentation information