Prolucid GUI

Legacy ProLuCID GUI by Yu (Tom) Gao, with a newer Python 3 rewrite kept in src/.

This repository now contains two related parts:

• The original desktop workflow and example assets used by the legacy project.
• A Python 3 rewrite of the GUI and command-line workflow under src/.

Both versions follow the same overall process:

1. Choose a FASTA database.
2. Choose one or more .ms2 files.
3. Generate search.xml.
4. Run ProLuCID.
5. Run DTASelect on the resulting .sqt files.

Repository Layout

.
|-- Prolucid_GUI.py
|-- Prolucid_GUI.exe
|-- example.ms2
|-- UniProt_human_with_reversed_sequence.fasta
|-- default_trypsin.prolucid_params
`-- src/
    |-- docs/
    |-- examples/
    |-- pyproject.toml
    `-- src/
        `-- prolucid_gui/

Python 3 Rewrite

The rewrite keeps the ProLuCID workflow but avoids embedding ProLuCID1_3.jar and DTASelect binaries in Python source code. Tool paths are supplied explicitly, which makes the project easier to inspect and maintain.

Requirements

• Python 3.10+
• Java available on the command line, or a direct path to java
• ProLuCID1_3.jar
• DTASelect classpath or extracted folder

Quick Start

Install from the rewrite folder:

cd src
pip install -e .

Run the GUI:

python -m prolucid_gui gui

Run the CLI help:

python -m prolucid_gui --help

Rewrite documentation:

• src/docs/command_line.md
• src/docs/gui_functions.md

Legacy GUI Example

The legacy GUI is a graphical interface for the ProLuCID database search engine for bottom-up proteomics protein identification. It takes MS2 files and a FASTA database as input, produces search outputs, and supports DTASelect-based filtering.

Prerequisites

Check that Java is installed:

java -version

To convert Thermo .raw files to .ms2, use RawConverter or ProteoWizard before running the search workflow.

Running the Example

On Windows:

1. Start Prolucid_GUI.exe.
2. Select the FASTA database, for example UniProt_human_with_reversed_sequence.fasta.
3. Select your java.exe path.
4. Select one or more .ms2 files, for example example.ms2.
5. Load parameters such as default_trypsin.prolucid_params, or set them manually.
6. Choose an output folder for search results.
7. Run ProLuCID and DTASelect.
8. Re-run DTASelect later if you want to change filtering only.

Authors

• Yu (Tom) Gao, Yates Lab
• Python 3 rewrite based on the legacy project in this repository

License

This tool is free to use for academic research purpose only.

Citation

Please cite the original ProLuCID paper:

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. Journal of Proteomics, 2015.