This collection of apps has been made to facilitate the analysis of mass spectrometry data. By installing this app, you are installing the following set of apps that work well together in workflows like this:
### Network Augmentation
After loading your binary interactions from mass spec, you can load additional interaction data using the following apps in this collection:
- [STRING app](https://apps.cytoscape.org/apps/stringapp)
### ID Mapping and Annotation
- Use built-in ID mapping via right-click on column header (if needed)
### Perform Analyses
- Cluster analysis with [clusterMaker2](https://apps.cytoscape.org/apps/clustermaker2)
- Functional enrichment with [BiNGO](https://apps.cytoscape.org/apps/bingo), [EnrichmentMap](https://apps.cytoscape.org/apps/enrichmentmap), or [ENViz](https://apps.cytoscape.org/apps/enviz)
### Resources to Help with Functional Interpretation
- [WikiPathways](https://apps.cytoscape.org/apps/wikipathways) and [ReactomeFI](https://apps.cytoscape.org/apps/reactomefiplugin) for pathway models
- [CyTargetLinker](https://apps.cytoscape.org/apps/cytargetlinker) for adding miRNA, TF and drug interactions
- [CyAnimator](https://apps.cytoscape.org/apps/cyanimator) to animate across time points or comparisons (if relevant)
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***Refer to the documentation and app store pages for each individual app for more details***
