alex123-tlg 0.7.0

ALEX123-TLG - GUI application for generating target lists for searching FTMS, MS2 and MS3 mass spectrometry data.

ALEX123-TLG (Target List Generator)

A GUI application for generating target lists for searching FTMS, MS2, and MS3 mass spectrometry data. Part of the ALEX123 lipidomics suite.

Features

• Multi-criterion filtering with OR logic combination
• Fragment filtering for MS2/MS3 tabs (AND logic)
• Chain index filtering (C/DB/OH) with min/max ranges and even/odd options
• Polarity filtering (positive/negative/neutral)
• Save and load filter configurations (.lxt files)
• Paginated data preview
• Cross-platform support (Windows, macOS, Linux)

Installation on Windows

1. Create a virtual environment. We recommend a shared venv for all ALEX123 modules:

cd C:\Users\user_name\alex123_software
python -m venv venv

2. Activate the virtual environment:

venv\Scripts\activate

3. Install the wheel (adjust the path if needed):

pip install C:\Users\user_name\Downloads\alex123_tlg-0.6.0-py3-none-any.whl

for Christer:

pip install C:\_MyStuff\ALEX123_software\alex123_tlg-0.6.2a0-py3-none-any.whl

All dependencies (PySide6, pandas) will be installed automatically.

Input Data Files

The application needs three TSV files: ms1.tsv, ms2.tsv, and ms3.tsv.

By default it looks for them in the platform-specific configuration directory:

OS	Directory
Windows	%APPDATA%\alex123-tlg\
macOS	~/Library/Application Support/alex123-tlg/
Linux	~/.config/alex123-tlg/

Copy ms1.tsv, ms2.tsv, and ms3.tsv into that directory.

Running the Application

Method	Command
Console script (after wheel install)	alex123-tlg
Python module (from source)	python -m app

On Windows, you can also create a .cmd launcher file with the following content and double-click it:

@echo off
cd /d "%~dp0"
"C:\Users\user_name\alex123_software\venv\Scripts\alex123-tlg.exe"

Replace C:\Users\user_name\alex123_software with the actual path to your virtual environment.

Usage

1. Select working directory -- choose the folder where output files will be saved
2. Switch tab -- select the MS1, MS2, or MS3 tab
3. Add filtering criteria -- configure filters for lipid class, species, adduct, category, and polarity
4. Set chain index filters (optional) -- adjust C, DB, and OH index ranges
5. Configure fragment filters (MS2/MS3 only) -- set fragment chain index filters
6. Click "Run" -- preview filtered results in the table
7. Click "Save" -- export the target list and filter configuration

Output Files

Saved to the selected working directory:

File	Description
targetlist_ms1.txt	Filtered MS1 target list (TSV)
targetlist_ms2.txt	Filtered MS2 target list (TSV)
targetlist_ms3.txt	Filtered MS3 target list (TSV)
targetlist_ms1.lxt	MS1 filter configuration (JSON)
targetlist_ms2.lxt	MS2 filter configuration (JSON)
targetlist_ms3.lxt	MS3 filter configuration (JSON)

Development

Run from source

uv pip install -r requirement.txt
python -m alex123_tlg

Linters

uv run isort . --check-only --diff
uv tool run ruff check .

Tests

uv pip install -r requirements-test.txt
uv run pytest tests/ -v

Build wheel

uv build --wheel