V1.2.2

New Features

• More normalization options

Installation

• Pull the latest docker image OR clone repository and use streamlit run tpp_solver_mt.py OR download tpp_solver.bat* and place it in a folder of your choice, then launch it

*Windows only

V1.2.1

New Features

• Benjamini-Hochberg FDR correction

Visualization Improvements

• Clearer graph layout
• Averaged replicate data per treatment curve fitting

Installation

• Pull the latest docker image OR clone repository and use streamlit run tpp_solver_mt.py OR download tpp_solver.bat* and place it in a folder of your choice, then launch it

*Windows only

V1.2.0

Major Changes

• Added Mann-Whitney U test for statistical significance testing
• Switched to per-replicate graph generation for improved data transparency and analysis
• Each protein plot now clearly displays individual replicates with their R² values

New Features

Statistical Testing

• Mann-Whitney U test between treatments
• P-value calculation for each protein
• Effect size calculations for each comparison
• Intuitive significance markers on volcano plots (*, **, ***)

Visualization Improvements

• Individual replicate plotting with distinct markers
• R² values shown directly on graphs
• Clear melting point indicators for each replicate
• Enhanced treatment group differentiation in plots

Bug Fixes

• Memory optimization for large datasets
• Improved curve fitting stability

Usage

No changes to input file formats required. Statistical test results are automatically included in the summary tables.

Coming Soon

• Clearer graph layout
• FDR correction

V1.1.3

What's Changed

• Switched GO ID database to DuckDB from SQLite
• Added interactive violin plots and histograms for melting point summary statistics
• Added custom normalization option
• Added visualization of melting point shifts by GO ID according to selected threshold
• Minor bug fixes and stabilization improvements
• R^2 statistic for curve fits

V1.1.0

Added GO ID scraper and respective database
Added Shapiro-Wilk normality test and transformations
Added GO annotation and standalone and integrated functions

V.1.0.0 release

TPP Solver Beta Release v1.0.0-beta

First release of the beta version of TPP Solver, a tool designed for conducting Thermal Proteome Profiling (TPP) analysis. This application allows researchers to upload intensity data from FragPipe along with metadata in CSV format, enabling analysis of protein thermal stability.

Key Features:

• Data Upload & Management: Upload FragPipe combined_prot TSV and metadata CSV files.
• Interactive Data Visualization: View and edit protein data with a user-friendly interface.
• Curve Fitting & Analysis: Performs sigmoidal curve fitting based on intensity of Max LFQ
• Data Imputation: Handles missing data points with imputation
• Downloadable Results: Download fitted curves in SVG format and summary table as CSV

Known Issues & Limitations:

• Performance: Possible delays with large datasets
• Compatibility: Currently tested with FragPipe output and specific CSV formats

Installation

Docker image: ghcr.io/username/tpp_solver:v1.0.0

You can pull the image using:

docker pull ghcr.io/username/tpp_solver:v1.0.0

Feedback & Contributions:

We encourage the community to test the app extensively and provide feedback. Please report any bugs, issues, or suggestions through the GitHub Issues tab.

V1.0.0-beta

TPP Solver Beta Release v1.0.0-beta

First release of the beta version of TPP Solver, a tool designed for conducting Thermal Proteome Profiling (TPP) analysis. This application allows researchers to upload intensity data from FragPipe along with metadata in CSV format, enabling analysis of protein thermal stability.

Key Features:

• Data Upload & Management: Upload FragPipe combined_prot TSV and metadata CSV files.
• Interactive Data Visualization: View and edit protein data with a user-friendly interface.
• Curve Fitting & Analysis: Performs sigmoidal curve fitting based on intensity of Max LFQ
• Data Imputation: Handles missing data points with imputation
• Downloadable Results: Download fitted curves in SVG format and summary table as CSV

Known Issues & Limitations:

• Performance: Possible delays with large datasets
• Compatibility: Currently tested with FragPipe output and specific CSV formats

Installation

Docker image: ghcr.io/username/tpp_solver:v1.0.0-beta

You can pull the image using:

docker pull ghcr.io/username/tpp_solver:v1.0.0-beta

Feedback & Contributions:

We encourage the community to test the app extensively and provide feedback. Please report any bugs, issues, or suggestions through the GitHub Issues tab.