MSstatsBioNet is an R/Bioconductor package for network analysis and enrichment of MSstats differential abundance results in the context of prior-knowledge biomolecular networks. It takes the output of MSstats (or MSstatsTMT / MSstatsPTM) differential abundance analysis, queries network databases for the interactions among the analyzed proteins, and filters, contextualizes, and visualizes the resulting subnetworks. Notably, it integrates with INDRA, a database of biological networks assembled from the literature using text mining, enabling interpretation of proteomic and phosphoproteomic results against past published knowledge.
MSstatsBioNet is part of the MSstats family of packages, developed and maintained by the Vitek Lab at Northeastern University. The package and its documentation are also available at msstats.org.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsBioNet")The development version can be installed directly from this repository:
remotes::install_github("Vitek-Lab/MSstatsBioNet")library(MSstatsBioNet)
# Example MSstats differential abundance results (groupComparison output)
input <- data.table::fread(system.file("extdata/groupComparisonModel.csv",
package = "MSstatsBioNet"))
# Retrieve the subnetwork of interactions among these proteins from INDRA
subnetwork <- getSubnetworkFromIndra(input)
head(subnetwork$nodes)
head(subnetwork$edges)
# Visualize the network (e.g. in Cytoscape, or export to HTML)
cytoscapeNetwork(subnetwork$nodes, subnetwork$edges)MSstatsBioNet works on differential abundance results, not raw search-tool
output. Its main entry point, getSubnetworkFromIndra(), accepts the
ComparisonResult table produced by the group-comparison functions across the
MSstats ecosystem:
| Upstream package | Function producing input |
|---|---|
| MSstats | groupComparison() |
| MSstatsTMT | groupComparisonTMT() |
| MSstatsPTM | groupComparisonPTM() |
The input table provides, per protein and comparison, the log2 fold change,
p-value, and adjusted p-value used for filtering and network coloring. UniProt
identifiers can be annotated with annotateProteinInfoFromIndra().
- Databases supported: INDRA
- Filtering options: p-value filter, context/topic-based filtering
(
filterSubnetworkByContext()) - Visualization options: Cytoscape Desktop (
cytoscapeNetwork()), in-browser preview (previewNetworkInBrowser()), standalone HTML export (exportNetworkToHTML()), and Shiny integration (cytoscapeNetworkOutput()/renderCytoscapeNetwork())
- MSstatsBioNet overview — getting started
- Cytoscape visualization
- Filter by context
- PTM analysis
- Official website: msstats.org
- Bioconductor package page and reference manual
- Questions about usage, statistical methods, or troubleshooting: please post to the MSstats Google Group. This is monitored by the development team and searchable, so it's the fastest way to get help and to see if your question has already been answered.
- Bug reports and feature requests for this repository: please open a GitHub issue.
If you use MSstatsBioNet, please cite:
- Wu A, Kohler D, Navada P, Robbins J, Boyle G, Boshart A, Karis K, Neefjes J, Konvalinka A, Sarthy J, Pino L, Gyori B, Vitek O. MSstatsBioNet: Integrating Statistical Analyses with Prior Knowledge Biomolecular Networks for Quantitative Proteomics and Phosphoproteomics. bioRxiv. 2026. DOI: 10.64898/2026.07.09.737605
MSstats development has been supported by the Chan Zuckerberg Initiative's Essential Open Source Software for Science.
MSstatsBioNet is released under the Artistic-2.0 license. However, its dependencies may have different licenses. Notably, INDRA is distributed under the BSD 2-Clause license, and INDRA's knowledge sources may have different licenses for commercial applications. Please refer to the INDRA README for more information on its knowledge sources and their associated licenses.