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Table 2 Results for the challenge (validation) data of the CASMI 2016 contest

From: Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

# Tools Top hits Top 5 Top 10 Top 20
1 CFM-ID + ID_sorted + DB + MS/MS Voting/consensus 181 194 201 204
2 CFM-ID + ID_sorted + MAGMa(+) + DB + MS/MS Voting/consensus 180 195 200 205
3 CFM-ID + ID_sorted + MAGMa(+) + MetFrag + DB + MS/MS Voting/consensus 180 194 200 204
4 CFM-ID + DB + MS/MS 180 193 199 201
5 MAGMa(+) + ID_sorted + DB + MS/MS Voting/consensus 180 193 197 201
6 CFM-ID + MAGMa(+) + DB + MS/MS Voting/consensus 180 192 195 202
7 MetFrag + MAGMa(+) + DB + MS/MS Voting/consensus 180 188 194 198
8 MAGMa(+) + DB + MS/MS 180 188 192 198
9 MetFrag + CFM-ID + MAGMa(+) + DB + MS/MS Voting/consensus 179 190 196 201
10 MetFrag + CFM-ID + DB + MS/MS Voting/consensus 178 192 199 203
11 CFM-ID + ID_sorted + MAGMa(+) + MetFrag + MS-FINDER + DB + MS/MS Voting/consensus 175 191 200 203
12 MetFrag + MS-FINDER + CFM-ID + DB + MS/MS Voting/consensus 175 189 194 200
13 MetFrag + MS-FINDER + CFM-ID + MAGMa(+) + DB + MS/MS Voting/consensus 175 189 194 200
14 MS-FINDER + ID_sorted + DB + MS/MS Voting/consensus 175 189 194 199
15 MS-FINDER + CFM-ID + MAGMa(+) + DB + MS/MS Voting/consensus 175 188 196 201
16 MetFrag + MS-FINDER + MAGMa(+) + DB + MS/MS Voting/consensus 175 186 191 197
17 MS-FINDER + MAGMa(+) + DB + MS/MS Voting/consensus 175 185 190 195
18 ID_SORTED + DB + MS/MS 174 195 198 204
19 MetFrag + ID_sorted + DB + MS/MS Voting/consensus 174 194 199 203
20 MS-FINDER + CFM-ID + DB + MS/MS Voting/consensus 174 189 195 201
21 MetFrag + DB + MS/MS 174 189 192 197
22 MetFrag + MS-FINDER + DB + MS/MS Voting/consensus 174 187 190 197
23 MS-FINDER + DB + MS/MS 174 184 185 191
24 MetFrag + CFM-ID + MAGMa(+) + DB Voting/consensus 151 184 192 198
25 CFM-ID + DB 151 183 191 197
26 MetFrag + MS-FINDER + CFM-ID + DB Voting/consensus 151 180 191 198
27 MS-FINDER + CFM-ID + MAGMa(+) + DB Voting/consensus 151 179 191 198
28 CFM-ID + MAGMa(+) + DB Voting/consensus 150 184 189 199
29 MetFrag + MAGMa(+) + DB Voting/consensus 150 181 189 194
30 MetFrag + MS-FINDER + MAGMa(+) + DB Voting/consensus 150 178 186 193
31 MS-FINDER + MAGMa(+) + DB Voting/consensus 150 174 183 191
32 MetFrag + CFM-ID + DB Voting/consensus 149 186 196 201
33 MAGMa(+) + DB 149 180 185 193
34 MS-FINDER + CFM-ID + DB Voting/consensus 149 179 189 199
35 MS-FINDER + DB 148 173 178 186
36 MetFrag + DB 147 185 188 194
37 MetFrag + MS-FINDER + DB Voting/consensus 147 178 184 193
38 ID_SORTED + DB 134 188 194 202
39 Randomize + DB + MS/MS 123 184 189 197
40 Randomize + DB 119 176 180 189
41 ID_SORTED 106 169 177 186
42 MetFrag in silico 53 92 111 137
43 MetFrag + MS-FINDER + CFM-ID in silico Voting/consensus 51 95 129 151
44 MetFrag + CFM-ID in silico Voting/consensus 47 102 129 153
45 MetFrag + MS-FINDER + CFM-ID + MAGMa(+) in silico Voting/consensus 46 97 128 152
46 MetFrag + CFM-ID + MAGMa(+) in silico Voting/consensus 42 104 126 150
47 CFM-ID + MAGMa(+) in silico Voting/consensus 39 94 123 148
48 MetFrag + MAGMa(+) in silico Voting/consensus 39 90 111 128
49 MetFrag + MS-FINDER + MAGMa(+) in silico Voting/consensus 38 79 117 138
50 MS-FINDER + CFM-ID + MAGMa(+) in silico Voting/consensus 34 97 127 147
51 MetFrag + MS-FINDER in silico Voting/consensus 33 76 103 125
52 MS-FINDER + MAGMa(+) in silico Voting/consensus 32 69 93 119
53 MS-FINDER + CFM-ID in silico Voting/consensus 30 76 110 139
54 CFM-ID in silico (dot product) 29 76 104 122
55 MAGMa(+) in silico 28 72 98 117
56 MS-FINDER in silico 23 57 79 93
57 Randomize 20 27 28 121
  1. ‘MetFragCL, CFM-ID, MAGMa+ and MS-FINDER’ designate results obtained by the in silico fragmentation software tools. ‘DB’ designates priority ranking by presence in chemical and biochemical databases. ‘MS/MS’ designates presence in MS/MS libraries based on >400 dot-product similarity. 208 MS/MS spectra of the CASMI 2016 training data were used