1 research outputs found
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, <sup>13</sup>C-metabolic flux
analyses (<sup>13</sup>C-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