alex123-tlg 0.7.1

This tool generates `target lists` (spectral libraries) for identifying lipid molecule and fragment m/z values in FTMS, MS2, and MS3 data.

ALEX123-TLG (Target List Generator)

This tool generates target lists (spectral libraries) for identifying lipid molecule and fragment m/z values in FTMS, MS2, and MS3 data.

Overview

ALEX123-TLG loads lipid tables exported for each MS level, lets you define filtering criteria (lipid class, species, adduct, category, polarity, and C/DB/OH chain indices), and exports a filtered "target list" together with a reusable filter configuration. MS2/MS3 additionally support a fragment filter, and MS1 supports isotope compilation.

Features

• Multi-criterion filtering combined with OR logic
• Fragment filtering for MS2/MS3 (applied as a final AND)
• Chain index filtering (C/DB/OH) with min/max ranges and even/odd options
• Polarity filtering (positive/negative/neutral)
• Isotope compilation for MS1 (¹³C isotopologues)
• Save and load filter configurations (.lxt files)
• Cross-platform (Windows, macOS, Linux)

Requirements

• Python >= 3.11

PySide6 and pandas are installed automatically as dependencies.

Installation

pip install alex123-tlg

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.

Usage

Run the application:

alex123-tlg

Or via the Python module:

python -m alex123_tlg

Then, in the app:

1. Select a working directory -- where output files are saved.
2. Switch to the MS1, MS2, or MS3 tab.
3. Add filtering criteria -- lipid class, species, adduct, category, polarity.
4. Set chain index filters (optional) -- C, DB, and OH index ranges.
5. Configure fragment filters (MS2/MS3 only).
6. Click "Run" to preview filtered results.
7. Click "Save" to 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)

License

alex123-tlg is licensed under the GNU General Public License v3.0 or later (full text). The LICENSE file is included in the package distribution.

This application uses PySide6 (Qt for Python) under the GNU Lesser General Public License v3.0 (LGPLv3). PySide6 and Qt are not part of this project; they are installed from PyPI and remain under their own license.