Extended Data Fig. 4. Comparison of fragmentation spectra for high-scoring incorrect hits from Fig. 4.

These correspond to compound pairs where COSMIC search resulted in an incorrect hit; would spectral library search be able to avoid these incorrect annotations? For three incorrect hits from Fig. 4 (a,b,h) there exist merged spectra; for the remaining six incorrect hits, no such data are available. Be reminded in all three cases (a,b,h), the true structure was not contained in the searched molecular structure database. Merged spectrum and structure of true structure shown top, merged spectrum and structure of incorrect hit bottom. Merged spectra were combined from 10 eV, 20 eV and 40 eV spectra as described in the Methods section. (a) Mirror plot for Fig. 4a, confidence 0.9596, cosine score 0.8566. (b) Mirror plot for Fig. 4b, confidence 0.9468, cosine score 0.9432. (c) Mirror plot for Fig. 4h, confidence 0.8942, cosine score 0.9968. In all three cases, the cosine score is above 0.85, and would result in a high-confidence but incorrect library search annotation if one of the spectra was in the library, the other our query. For (c) we argue that no method could possibly distinguish between these structures based on the MS/MS data. Merged spectra: (a) correct NIST 1210761/62/64, incorrect hit NIST 1215622/23/27; (b) correct NIST 1617825/29/34, incorrect hit NIST 1386465/69/74; (c) correct NIST 1418771/73/80, incorrect hit NIST 1375293/295/301.