1518 performed on the Agilent 120 Infinity II UHPLC connected to an Agilent
   Quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA, USA).
   The LC column used was a Scherzo SM-C18 column (100 μm,
   08.00) (Agilent Technologies). The mass spectrometric conditions
   and multiple reaction monitoring transitions were the same as previously
   300 Å, 18 column (2.0 mm, 3 μm) (Imtakt, Kyoto, Japan) at 40 °C with a gradient of 0.350 mL/min and 5 μL, respectively.
   The following gradients were used: (A) 0.1% formic acid and
   (B) 0.1% formic acid in acetonitrile. The column
   gradient was as follows: 0–15 min, 0–100% B; 15–16 min, 100% B; 16–17 min,
   0% B; 17–20 min, 5% B. The MS parameters were as follows: gas temperature, 200 °C;
   gas flow, 15 L/min; nebulizer pressure, 20 psi; sheath gas temperature, 350
   °C; capillary voltage and fragmentation voltage were
   optimization. The dynamic MRM transitions. The optimized collision energies and MRM
   transitions for each metabolite are listed in [144]Table S2. The quantification was performed
   C-2-amphetamine was used as an internal standard for quantification.
   The raw data were processed and analyzed using MassHunter Quantitative
   Analysis B.04
   (Agilent Technologies, Santa Clara, CA, USA). All of the metabolites
   14.1 (Umetrics, Umeå, Sweden) software to determine the clustering and
   pattern recognition of the dataset and to evaluate the overall differences between the
   metabolomic data were normalized using generalized log transformation and mean-centering. The
   multivariate analysis was conducted by OPLS-DA. PLS-DA and OPLS-DA were
   based on R^2 and Q^2 values, which were
   estimates of the goodness-of-fit and predictive ability of the
   model. The univariate analysis were determined using the Mann–Whitney
   Wilcoxon test and Wilcoxon rank-sum test. Statistical analysis
   categorical variables. Multiple comparisons were adjusted for false discovery
   using the Benjamini-Hochberg multiple comparison correction. Metabolite sets
   enrichment analysis. The ROC curve and Youden index were applied to evaluate the diagnostic values of the
   basis of the AUC and Youden index for further validation. The validation analysis was carried out
   using Dunn’s test. The ORs and corresponding 95%
   CIs for the risk of cervical cancer. The combined effects of
   HPV and metabolites was performed using the seven selected metabolites. The combined
   analyzed using MetPA and the enrichment analysis. The data were analyzed
   using the MetPA 4.0 (Xia Lab, Montreal, Canada). The
   Canada). Metabolic pathways were assessed using MetPA software and were enriched for the
   assess the association between the metabolites and the risk of cervical cancer. The
   adjustment for the covariates. All of the statistical tests were conducted using the SPSS 22.0
   and alcohol consumption using SPSS Statistics 22.0 software
   (IBM, Armonk, NY, USA). The metabolites.
   ^13C[6]-phenylalanine was used as an internal
   standard. The metabolites and the cervical cancer risk using
   multivariate model. The data were analyzed using R 3.6.3. The
   data were analyzed using the SPSS software.

   The statistical analyses were performed using the R platform (Version 3.6.3 and the SPSS software 22.0.

---

### Answers to the Questions:

1. **What tool was used for pathway enrichment analysis?**
   - MetaboAnalyst 4.0.

2. **Was a tool version number provided?**
   - Not described.

3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?**
   - Not described.

4. **Was a background gene list defined for pathway enrichment analysis?**
   - Not described.

5. **What statistical test was used for enrichment analysis?**
   - Not described.

6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?**
   - Not described.