Tackling CASMI 2012: Solutions from MetFrag and MetFusion
Abstract
:1. Introduction
2. Methods
2.1. Spectra Processing and Neutral Mass Heuristics
2.2. Eliminating Redundant Candidates
2.3. In silico Fragmentation with MetFrag
2.4. MetFusion: Integration of MetFrag with Spectral Libraries
3. Results and Discussion
3.1. MetFrag
Natural Product Challenges | Environmental Challenges | ||||||||
---|---|---|---|---|---|---|---|---|---|
Chall. | #Cand. | Rank | RRP | MLS | RRP | Chall. | #Cand. | Rank | RRP |
10 | 447 | 260 | 0.441 | ||||||
1 | 994 | 5 | 0.996 | 4 | 0.997 | 11 | 465 | 23 | 0.976 |
2 | 248 | 3 | 0.992 | 3 | 0.992 | 12 | 1531 | 36 | 0.978 |
3 | 1094 | 12 | 0.990 | 9 | 0.993 | 13 | 1031 | 5 | 0.998 |
4 | 2234 | 547 | 0.757 | 454 | 0.797 | 14 | 125 | 27 | 0.810 |
5 | 2891 | 988 | 0.679 | 1238 | 0.573 | 15 | 1825 | 173 | 0.907 |
6 | 1860 | 1860 | 0.439 | 281 | 0.850 | 16 | 1948 | 1948 | 0.453 |
17 | 475 | 15 | 0.970 | ||||||
Median | 1477 | 280 | 0.874 | 145 | 0.921 | 753 | 32 | 0.939 |
Challenge | Trivial name | InChIKey (first block) | MLS | MLS rank |
---|---|---|---|---|
1 | Kanamycin A | SBUJHOSQTJFQJX | 0.508 | 47 |
2 | 1,2-Bis-O-sinapoyl-beta-D-glucoside | KQDOTXAUJBODDM | 0.716 | 35 |
3 | Glucolesquerellin | ZAKICGFSIJSCSF | 0.474 | 3 |
4 | Escholtzine | PGINMPJZCWDQNT | 0.436 | 439 |
5 | Reticuline | BHLYRWXGMIUIHG | 0.296 | 1209 |
6 | Rhoeadine | XRBIHOLQAKITPP | 0.374 | 132 |
3.2. MetFusion
Natural Product Challenges | Environmental Challenges | ||||||||
---|---|---|---|---|---|---|---|---|---|
Chall. | #Cand. | Rank | Max. TS | RRP | Chall. | #Cand. | Rank | Max. TS | RRP |
10 | 1085 | 981 | 0.40 | 0.096 | |||||
1 | 2229 | 1 | 1.0 | 1.0 | 11 | 1444 | 170 | 0.28 | 0.883 |
2 | 625 | 4 | 0.93 | 0.995 | 12 | 3772 | 136 | 0.28 | 0.964 |
3 | 2945 | 14 | 0.99 | 0.995 | 13 | 3344 | 1 | 1.0 | 1.0 |
4 | 4219 | 74 | 0.84 | 0.983 | 14 | 507 | 3 | 1.0 | 0.996 |
5 | 4280 | 1426 | 0.42 | 0.667 | 15 | 3394 | 1 | 1.0 | 1.0 |
6 | 6175 | 25 | 0.79 | 0.996 | 16 | 4427 | 1351 | 0.33 | 0.695 |
17 | 1848 | 88 | 0.35 | 0.953 | |||||
Median | 3582 | 20 | 0.89 | 0.995 | 2596 | 112 | 0.38 | 0.959 |
4. Conclusions
Acknowledgements
Conflict of Interest
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Appendix
A. Additional MetFrag Results
Natural Product Challenges | Environmental Challenges | ||||||||
---|---|---|---|---|---|---|---|---|---|
Chall. | #Cand. | Rank | RRP | MLS | RRP | Chall. | #Cand. | Rank | RRP |
10 | 257 | 170 | 0.377 | ||||||
1 | 9 | 5 | 0.500 | 4 | 0.625 | 11 | 104 | 9 | 0.961 |
2 | 43 | 1 | 1.000 | 1 | 1.000 | 12 | 950 | 26 | 0.975 |
3 | 2 | 2 | 0.500 | 1 | 1.000 | 13 | 22 | 4 | 0.929 |
4 | 2005 | 534 | 0.735 | 444 | 0.779 | 14 | 111 | 19 | 0.859 |
5 | 2429 | 754 | 0.714 | 920 | 0.623 | 15 | 1789 | 172 | 0.905 |
6 | 1250 | 1250 | 0.416 | 234 | 0.814 | 16 | 1397 | 1397 | 0.438 |
17 | 415 | 15 | 0.966 | ||||||
Median | 646 | 270 | 0.607 | 119 | 0.797 | 336 | 22.5 | 0.917 |
B. Spectral Merging
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Ruttkies, C.; Gerlich, M.; Neumann, S. Tackling CASMI 2012: Solutions from MetFrag and MetFusion. Metabolites 2013, 3, 623-636. https://doi.org/10.3390/metabo3030623
Ruttkies C, Gerlich M, Neumann S. Tackling CASMI 2012: Solutions from MetFrag and MetFusion. Metabolites. 2013; 3(3):623-636. https://doi.org/10.3390/metabo3030623
Chicago/Turabian StyleRuttkies, Christoph, Michael Gerlich, and Steffen Neumann. 2013. "Tackling CASMI 2012: Solutions from MetFrag and MetFusion" Metabolites 3, no. 3: 623-636. https://doi.org/10.3390/metabo3030623