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Conduit-Summit is an R Shiny application that provides a comprehensive set of tools for analyzing metaproteomics data obtained using data-independent acquisition (DIA). It is designed to be accessible even for non-coders — no programming required.
Metaproteomics data are inherently complex, and there are many non-trivial ways to approach the analysis. Conduit-Summit supports a broad range of analyses, enabling users to extract insights from their data more quickly, easily, and reproducibly than ever before.
Most existing tools offer limited flexibility when it comes to handling metadata — such as filtering data based on a variable, coloring plots by a metadata field, or fitting flexible statistical models. Conduit-Summit aims to fill this gap with a comprehensive and user-friendly solution for metaproteomic data analysis.
If you're working with DIA metaproteomics data, Conduit-Ascent and Conduit-Summit together can streamline your analysis from raw data to publication-quality figures.
Conduit-Ascent is a Snakemake workflow that handles the computationally intensive processing steps:
- Generates a tailored search database
- Annotates proteins and taxa using various databases
- Identifies and quantifies spectra via DIA-NN
- Produces the
conduit.rdsoutput file
The conduit.rds file contains everything Conduit-Summit needs for downstream analysis: database statistics, protein identifications, taxonomic summaries, DIA-NN QC metrics, and experimental metadata — all wrapped in a structured QFeatures object.
Conduit-Summit allows users to:
-
Upload data directly from Conduit-Ascent (
.rdsfile, up to 500 MB) - Explore database coverage — assess detected proteins per organism relative to the search database
- Review DIA-NN QC metrics from the search
- Explore sample metadata associated with each sample
- Filter results based on user-specified sample- and feature-level criteria
- Browse the processed assay data interactively
-
Analyze data with a full suite of tools:
- QC plots (feature numbers, missing values, sample correlation, intensity distributions, density plots)
- PCA biplot
- Heatmaps (interactive and static)
- Relative abundance visualization
- Custom exploratory plots (scatter, bar, line, boxplot, violin, histogram)
- Differential expression statistics via limma
- Functional enrichment analysis (GSEA / ORA) for GO terms, KEGG, and taxonomic levels
- KEGG pathway visualization
- Machine learning classification and prediction (LASSO, random forest, XGBoost)
- Traverse feature hierarchies across assay levels (precursor → peptide → protein → taxon)
- Chat with an AI assistant to explore and interpret your data using natural language (supports Anthropic, OpenAI, Google Gemini, and local Ollama models)
- Generate publication-quality figures in multiple formats (PDF, PNG, SVG, JPEG, TIFF, EPS)
You need the conduit.rds file output from the Conduit-Ascent workflow. Upload it on the About tab to unlock all downstream analysis.
Under the hood, this file is a Conduit object (as defined in the conduitR package). It contains a QFeatures object with all sample metadata (colData), feature data (rowData), and multiple assay levels — precursors, peptides, protein groups, and taxonomic/functional aggregations (domain through species, GO terms, KEGG pathways).
This wiki mirrors the layout of the Conduit-Summit app. Each tab in the app corresponds to a page in the wiki. The header controls (Plot Options, Aggregation Level, Advanced Settings) have their own dedicated pages.
| Wiki Page | App Tab |
|---|---|
| About | About (includes file upload) |
| AI Assistant | AI |
| Database | Database |
| DIA-NN QC | DIA-NN QC |
| View Metadata | View Metadata |
| Filter Data | Filter Data |
| View Assay | View Assay |
| Analysis | Analysis |
| Traverse | Traverse |
| Help | Help |
| Plot Options | Header: Plot Options |
| Aggregation Level | Header: Aggregation Level |
| Advanced Settings | Header: Advanced Settings |