Recent innovations from the literature may be swiftly integrated into Compound Discoverer via custom scripting nodes. One example is the orthogonal MS1 PFAS discrimination tool adapted from (Kaufman et al. 2022). This optional tool enhances the newly released PFAS Unknown ID w Database Searches and Molecular Networks workflow, enabling the generation of PFAS discrimination plots. This approach bypasses the need for fragmentation data. Instead, it uses the measured A0 and A1 distribution as inputs to approximate the number of carbons enabling the creation of new m/C (molecular mass divided by the number of carbon atoms) and md/C (mass defect divided by the number of carbon atoms) ratios. When these new ratios are plotted via onboard visualization tools, PFAS-containing molecules cluster on the bottom right quadrant, as shown below.
The number of carbons assigned by this node is independent of other annotation sources present within CD. It enables a truly orthogonal approach for validating PFAS captured via fragmentation-based filtering approaches and retaining unknown compounds presenting PFAS characteristics. The selectivity of this approach ensures the retention of a limited number of targets displayed as gray circles within the region of interest, making them amenable to further investigation.
Compounds lacking fragmentation data and those whose top formula assignment lacked a minimum number of fluorine atoms, but contained an alternate predicted composition, ChemSpider match, or mass list match fulfilling this requirement, may be re-examined using this tool. The clustering below validates findings from the fragment-based filtering approach since retained compounds that received check marks cluster only on the bottom right appearing as light blue circles within the region of interest. Checked compounds occurring outside this region should face scrutiny, and the reason for their location should be understood. This tool is unsuitable for compounds where no A1 is detected as they plot to the origin despite some targets being putatively identified as PFAS via the workflow’s fragmentation-based filtering scheme. PFAS, where multiple carbon atoms are substituted by oxygen or other atoms in the structure’s backbone, also occur outside the region of interest and are omitted as edge cases. These compounds appear higher to the upper left than normal PFAS with unsubstituted CF2 chains. The following filtering schema focusing only on the region where most of the traditional PFAS reside may be applied.
This filter leverages new Max F columns also enabled by this scripting node indicating the formula with the maximum number of fluorine atoms within all the annotation sources to prevent formula miss assignments and elucidate previously missed targets.
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The PFAS scripting node and installation instructions are available below.
Thermo Fisher Scientific
United States
