pepMAP

pepMAP is a web-based application for visualizing peptide mappings onto protein sequences. It supports input from both FragPipe and DIA-NN reports, providing an interactive interface to explore peptide coverage, modifications, and protein features.

Features

• Support for FragPipe and DIA-NN Inputs: Upload peptide reports from FragPipe or DIA-NN to visualize peptide mappings on proteins.

• Interactive Visualization: Explore peptide coverage with an intuitive interface powered by Plotly.

• Protein Feature Integration: Fetch and display protein domains, binding sites, modified residues, and variants from UniProt.

• Multi-User Sessions: Supports multiple users simultaneously with isolated sessions.

• Scheduled Session Deletion: Automatically clears sessions daily to manage resources efficiently.

Installation

To run pepMAP locally, follow these steps:

1. Clone the Repository

git clone https://github.com/npinter/pepMAP.git
cd pepMAP

2. Create a Conda Environment

Create a new Conda environment named pepMAP with the required packages:

conda create -n pepMAP -c conda-forge python=3.9 numpy==1.26.4 pandas==2.2.2 plotly==5.21.0 requests==2.31.0 flask==3.0.3 flask-caching==2.1.0 flask-session==0.8.0 apscheduler==3.10.4

3. Run the Application

Activate the Conda Environment

conda activate pepMAP

Start the Flask application:

(pepMAP) python app.py

By default, the application runs on http://localhost:7007.

Usage

1. Upload Files: Upload your peptide report (from FragPipe or DIA-NN) and FASTA file used in the search.

2. Search Proteins: Enter a UniProt ID or gene symbol to visualize peptide mappings.

License

This project is licensed under the MIT License.

Note

• Ensure that you have an active internet connection, as the application fetches protein features from the UniProt API.
• The application schedules daily deletion of session data to manage server resources effectively.