References

1.

Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. & Siuzdak, G. XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. Analytical Chemistry 78, 779–787 (2006).

2.

Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R. & Neumann, S. CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets. Analytical Chemistry 84, 283–289 (2012).

3.

Tsugawa, H. et al. A lipidome atlas in MS-DIAL 4. Nature Biotechnology 38, 1159–1163 (2020).

4.

Zhou, Z. et al. Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking. Nature Communications 13, 6656 (2022).

5.

Liu, Y. et al. A widely distributed gene cluster compensates for uricase loss in hominids. Cell 186, 3400–3413.e20 (2023).

6.

Schmid, R. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nature Biotechnology 41, 447–449 (2023).

7.

Shen, X. et al. TidyMass an object-oriented reproducible analysis framework for LC–MS data. Nature Communications 13, (2022).

8.

Liu, Y. et al. Gut bacteria degrade purines via the 2,8-dioxopurine pathway. Nature Microbiology 10, (2025).