biostudies-literatureRudolph JDEuropean Research CouncilH2020 Future and Emerging Technologies2052-2064https://www.ebi.ac.uk/biostudies/studies/S-EPMC6578358biostudies-literatureUnknown18(5)Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affinity purification experiments, but networks are also used to explore proteomics data. PerseusNet supports the biomedical researcher for both modes of data analysis with a multitude of activities. For affinity purification, a volcano-plot-based statistical analysis method for network generation is featured which is scalable to large numbers of baits. For posttranslational modifications of proteins, such as phosphorylation, a collection of dedicated network analysis tools helps Journal of proteome researchA Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis.PMC6578358686547318987Cox JRudolph JDfalseA Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis.Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affinity purification experiments, but networks are also used to explore proteomics data. PerseusNet supports the biomedical researcher for both modes of data analysis with a multitude of activities. For affinity purification, a volcano-plot-based statistical analysis method for network generation is featured which is scalable to large numbers of baits. For posttranslational modifications of proteins, such as phosphorylation, a collection of dedicated network analysis tools helps 2019-01-01T00:00:00Z2019 May2026-05-07T13:29:49.7Z2025-05-29T21:45:46.129ZS-EPMC65783583093157010.1021/acs.jproteome.8b00927