Statistical analysis of dissolved organic matter characterized by high-resolution mass spectrometry
iDOM is a multifunctional tool that facilitates basic analyses, such as the calculation of molecular traits, the assignment of molecular classes, and the evaluation of chemical diversity and dissimilarity. It also includes functions for advanced analyses to quantify the assembly processes of DOM assemblages, the effect of molecular dark matter on DOM molecular interactions, and the associations between DOM molecules and microbial taxa.
We expect that iDOM will serve as a comprehensive pipeline for DOM statistical analyses and bridge the gap between chemical characterization and ecological interpretation.
Package maintainer: Jianjun Wang ([email protected])
Developers: Ang Hu, Fanfan Meng
You can install the development version of iDOM from GitHub with:
# install.packages("devtools")
devtools::install_github("jianjunwang/iDOM")Installing packages in R from zip source. You may have downloaded iDOM in zip or tar.gz format. In order to install the package from a local zip file, you just need to call the install.packages function with arguments repos = NULL and type = “source”.
install.packages("file_path/package_file_name.extension",repos = NULL, type = "source")commProc: Quantifies the relative influences of deterministic and stochastic processes in the assembly of DOM assemblages.
iDME: Quantifies the effect of molecular dark matter on DOM assemblages by constructing co-occurrence networks based on the presence and absence of dark matter.
H2: Calculates the network-level specialization of all interacting trophic levels in DOM-microbe bipartite networks, including full, negative and positive networks.
iCER: Calculates the indicator of compositional-level environmental response to assess the thermal response of DOM.
F Meng, A Hu, K-S Jang, and J Wang. 2025. iDOM: Statistical analysis of dissolved organic matter characterized by high-resolution mass spectrometry. mLife 4:319-331. https://doi.org/10.1002/mlf2.70002
A Hu, K-S Jang, A J Tanentzap, W Zhao, J T Lennon, J Liu, M Li, J Stegen, M Choi, Y Lu, X Feng, and J Wang. 2024. Thermal responses of dissolved organic matter under global change. Nature Communications 15:576. https://www.nature.com/articles/s41467-024-44813-2
A Hu, M Choi, A J Tanentzap, J Liu, K-S Jang, J T Lennon, Y Liu, J Soininen, X Lu, Y Zhang, J Shen, and J Wang. 2022. Ecological networks of dissolved organic matter and microorganisms under global change. Nature Communications 13:3600. https://www.nature.com/articles/s41467-022-31251-1
A Hu, F Meng, A J Tanentzap, K-S Jang, and J Wang. 2023. Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change. Environmental Science & Technology 57:761-769. https://pubs.acs.org/doi/10.1021/acs.est.2c05052
A Hu, K-S Jang, F Meng, J Stegen, A J Tanentzap, M Choi, J T Lennon, J Soininen, and J Wang. 2022. Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition. Environmental Science & Technology 56:10504-10516. https://pubs.acs.org/doi/abs/10.1021/acs.est.2c01432
F Meng, A Hu, K-S Jang, and J Wang. 2025. iDOM: Statistical analysis of dissolved organic matter characterized by high-resolution mass spectrometry. mLife 4:319-331. https://doi.org/10.1002/mlf2.70002
A Hu, L Han, X Lu, G Zhang and J Wang. 2024. Global patterns and drivers of dissolved organic matter across Earth systems: Evidence from H/C and O/C ratios. Fundamental Research 5:2121-2132. https://doi.org/10.1016/j.fmre.2023.11.018
A Hu, Y Cui, S Bercovici, A J Tanentzap, J T Lennon, X Lin, Y Yang, Y Liu, H Osterholz, H Dong, Y Lu, N Jiao, and J Wang. 2024. Photochemical processes drive thermal responses of dissolved organic matter in the dark ocean. bioRxiv. https://doi.org/10.1101/2024.09.06.611638
L Han, A Hu, H L Mzuka, X Chen, J Shen and J Wang. 2025. Molecular properties of dissolved organic matter across Earth systems: A meta-analysis. Journal of Earth Science 36:2674-2688. https://link.springer.com/article/10.1007/s12583-024-0061-9
Y Cui, A Hu, J Stegen, and J Wang. 2026. Habitat Affinity of Riverine Dissolved Organic Matter Linked to Molecular Traits. Global Change Biology 32:e70736. https://onlinelibrary.wiley.com/doi/10.1111/gcb.70736?af=R