Isotope Cluster-Based Compound Matching in Gas Chromatography/Mass Spectrometry for Non-Targeted Metabolomics

Gas chromatography coupled to mass spectrometry (GC/MS) has emerged as a powerful tool in metabolomics studies. A major bottleneck in current data analysis of GC/MS-based metabolomics studies is compound matching and identification, as current methods generate high rates of false positive and false -negative identifications. This is especially true for data sets containing a high amount of noise. In this work, a novel spectral similarity measure based on the specific fragmentation patterns of electron impact mass spectra is proposed. An important aspect of these algorithmic methods is the handling of noisy data. The performance of the proposed method compared to the dot product, the current gold standard, was evaluated on a complex biological data set. The analysis results showed significant improvements of the proposed method in compound matching and chromatogram alignment compared to the dot product

Fragment Formula Calculator (FFC): Determination of Chemical Formulas for Fragment Ions in Mass Spectrometric Data

The accurate determination of mass isotopomer distributions (MID) is of great significance for stable isotope-labeling experiments. Most commonly, MIDs are derived from gas chromatography/electron ionization mass spectrometry (GC/EI-MS) measurements. The analysis of fragment ions formed during EI, which contain only specific parts of the original molecule can provide valuable information on the positional distribution of the label. The chemical formula of a fragment ion is usually applied to derive the correction matrix for accurate MID calculation. Hence, the correct assignment of chemical formulas to fragment ions is of crucial importance for correct MIDs. Moreover, the positional distribution of stable isotopes within a fragment ion is of high interest for stable isotope-assisted metabolomics techniques. For example, ¹³C-metabolic flux analyses (¹³C-MFA) are dependent on the exact knowledge of the number and position of retained carbon atoms of the unfragmented molecule. Fragment ions containing different carbon atoms are of special interest, since they can carry different flux information. However, the process of mass spectral fragmentation is complex, and identifying the substructures and chemical formulas for these fragment ions is nontrivial. For that reason, we developed an algorithm, based on a systematic bond cleavage, to determine chemical formulas and retained atoms for EI derived fragment ions. Here, we present the fragment formula calculator (FFC) algorithm that can calculate chemical formulas for fragment ions where the chemical bonding (e.g., Lewis structures) of the intact molecule is known. The proposed algorithm is able to cope with general molecular rearrangement reactions occurring during EI in GC/MS measurements. The FFC algorithm is able to integrate stable isotope labeling experiments into the analysis and can automatically exclude candidate formulas that do not fit the observed labeling patterns. We applied the FFC algorithm to create a fragment ion repository that contains the chemical formulas and retained carbon atoms of a wide range of trimethylsilyl and <i>tert</i>-butyldimethylsilyl derivatized compounds. In total, we report the chemical formulas and backbone carbon compositions for 160 fragment ions of 43 alkylsilyl-derivatives of primary metabolites. Finally, we implemented the FFC algorithm in an easy-to-use graphical user interface and made it publicly available at http://www.ffc.lu