posted on 2016-07-15, 00:00authored byHiroshi Tsugawa, Tobias Kind, Ryo Nakabayashi, Daichi Yukihira, Wataru Tanaka, Tomas Cajka, Kazuki Saito, Oliver Fiehn, Masanori Arita
Compound identification from accurate
mass MS/MS spectra is a bottleneck
for untargeted metabolomics. In this study, we propose nine rules
of hydrogen rearrangement (HR) during bond cleavages in low-energy
collision-induced dissociation (CID). These rules are based on the
classic even-electron rule and cover heteroatoms and multistage fragmentation.
We evaluated our HR rules by the statistics of MassBank MS/MS spectra
in addition to enthalpy calculations, yielding three levels of computational
MS/MS annotation: “resolved” (regular HR behavior following
HR rules), “semiresolved” (irregular HR behavior), and
“formula-assigned” (lacking structure assignment). With
this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in
the MassBank database and 84.8% of a total of 36370 MS/MS fragment
ions in the GNPS database were (semi-) resolved by predicted bond
cleavages. We also introduce the MS-FINDER software for structure
elucidation. Molecular formulas of precursor ions are determined from
accurate mass, isotope ratio, and product ion information. All isomer
structures of the predicted formula are retrieved from metabolome
databases, and MS/MS fragmentations are predicted in silico. The structures
are ranked by a combined weighting score considering bond dissociation
energies, mass accuracies, fragment linkages, and, most importantly,
nine HR rules. The program was validated by its ability to correctly
calculate molecular formulas with 98.0% accuracy for 5063 MassBank
MS/MS records and to yield the correct structural isomer with 82.1%
accuracy within the top-3 candidates. In a test with 936 manually
identified spectra from an untargeted HILIC-QTOF MS data set of human
plasma, formulas were correctly predicted in 90.4% of the cases, and
the correct isomer structure was retrieved at 80.4% probability within
the top-3 candidates, including for compounds that were absent in
mass spectral libraries. The MS-FINDER software is freely available
at http://prime.psc.riken.jp/.