Table 1.

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

	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

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 ${\mathit{\omega }}_{\mathrm{Frag}}=0.67$ and ${\mathit{\omega }}_{\mathrm{CFM}\text{-}\mathrm{ID}}=0.33$. The expected ranks, which partially account for equally scored candidates as calculated in [16], are shown in the lower part of the table