![]() Candidate compounds were retrieved from PubChem using the exact mass. used Mass Frontier 4 to predict the tandem MS spectra of 102 test compounds, which were analysed using a Micromass Q-TOF II in positive mode, to identify the measured compound and its structure. For some compounds, MassFrontier 5 is not able to identify any fragments in negative mode. A different approach towards identification is the interpretation of the measured spectra, usually with regard to the known (or hypothetical) molecular structure.įragmenter with a rule set like the commercial tools ACD Fragmenter and Mass Frontier generate fragments based on cleavage rules known from the literature, in both cases the algorithmic details are not published. Large spectral libraries of measured reference spectra exist for GC/MS, such as the commercial NIST library '08 (Gaithersburg, MD) or the GMD, but for ESI-tandem MS spectral libraries are still few and comparably small. In tandem MS, the molecules are interacting with a collision gas at specified kinetic energies, hence the name collision induced dissociation. In addition to the exact mass, tandem MS spectra provide additional structural hints, providing a fingerprint of the measured molecule. ![]() ![]() The main bottleneck in the interpretation of metabolomics experiments is the identification of compounds. Various ionisation methods are commonly used, such as electron impact (EI) used with gas chromatography (GC/MS), or the soft electrospray ionisation (ESI), which is employed in LC/ESI-MS systems. Mass spectrometry has become the analytical method of choice in metabolomics research. The web frontend allows the end-user to analyse single spectra and browse the results, whereas the web service and console application are aimed to perform batch searches and evaluation. MetFrag is available through a web application, web services and as java library. Our tool MetFrag improves the identification of unknown substances from tandem MS spectra and delivers better results than comparable commercial software. With today's massive general purpose compound libraries we obtain dozens of very similar candidates, which still allows a confident estimate of the correct compound class. We presented a method that is able to identify small molecules from tandem MS measurements, even without spectral reference data or a large set of fragmentation rules. The in silico fragmentation requires less than a second to process a molecule, and MetFrag performs a search in KEGG or PubChem on average within 30 to 300 seconds, respectively, on an average desktop PC. Especially for large compound libraries, the candidates with a good score show a high structural similarity or just different stereochemistry, a subsequent clustering based on chemical distances reduces this redundancy. Compared to a previously published study, MetFrag obtained better results than the commercial MassFrontier software. In the evaluation MetFrag was able to rank most of the correct compounds within the top 3 candidates returned by an exact mass query in KEGG. We created the MetFrag suite to obtain a candidate list from compound libraries based on the precursor mass, subsequently ranked by the agreement between measured and in silico fragments. Compound libraries such as PubChem or KEGG describe a larger number of compounds, which can be used to compare their in silico fragmentation with spectra of unknown metabolites. ![]() In addition to the precursor mass, tandem MS spectra carry informative fragment peaks, but the coverage of spectral libraries of measured reference compounds are far from covering the complete chemical space. The identification of unknown compounds is the main bottleneck. ![]()
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