Exploring applications of non-targeted analysis in the characterization of the prenatal exposome

Abstract

Capturing the breadth of chemical exposures in utero is critical in understanding their long-term health effects for mother and child. We explored methodological adaptations in a Non-Targeted Analysis (NTA) pipeline and evaluated the effects on chemical annotation and discovery for maternal and infant exposure. We focus on lesser-known/underreported chemicals in maternal and umbilical cord serum analyzed with liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). The samples were collected from a demographically diverse cohort of 296 maternal-cord pairs (n = 592) recruited in San Francisco Bay area. We developed and evaluated two data processing pipelines, primarily differing by detection frequency cut-off, to extract chemical features from non-targeted analysis (NTA). We annotated the detected chemical features by matching with EPA CompTox Chemicals Dashboard (n = 860,000 chemicals) and Human Metabolome Database (n = 3140 chemicals) and applied a Kendrick Mass Defect filter to detect homologous series. We collected fragmentation spectra (MS/MS) on a subset of serum samples and matched to an experimental MS/MS database within the MS-Dial website and other experimental MS/MS spectra collected from standards in our lab. We annotated ~72 % of the features (total features = 32,197, levels 1-4). We confirmed 22 compounds with analytical standards, tentatively identified 88 compounds with MS/MS spectra, and annotated 4862 exogenous chemicals with an in-house developed annotation algorithm. We detected 36 chemicals that appear to not have been previously reported in human blood and 9 chemicals that were reported in less than five studies. Our findings underline the importance of NTA in the discovery of lesser-known/unreported chemicals important to characterize human exposures.

Keywords: Data pipeline; Exposome; High resolution mass spectrometry; Kendrick mass defect; Non-targeted analysis; Prenatal exposure.

Figure 1:

Overall NTA Workflow schematic for extracting and annotating chemical features: Sample and standard measurement, data processing, and chemical annotation approach. ** Non-Targeted Analysis Data Process is described in Figure S1.

Figure 2:

Feature plot of homologous series candidates as a function of m/z and RT for A) CF₂, B) C₂H₄O, C) CH₂ (positive), and D) CH₂ (negative). Features with connected lines are the identified homologous series. Dashed lines in D) show 2 potential routes of the homologous series.

Figure 3:

A) Percentage of total features that are detectable in serum samples and B) the percentage of feature detectability in maternal/cord pairs (e.g., if feature is detectable in maternal and cord pair or not, then feature = 1, if feature is found in either maternal or cord, but not the other, then feature = 0).