ALEX123 Extractor

A PySide6 GUI application for mass spectrometry data extraction and offline lock mass recalibration.

Overview

ALEX123 Extractor processes spectral files against targetlists to find peaks, calculate calibration offsets, and generate detailed output tables. It supports offline lock mass recalibration using known reference ions, targetlist processing with optional calibration correction, and gap analysis for quality control. MS1, MS2, and MS3 data are handled in separate tabs, with MS2/MS3 organized by precursor m/z directories.

Features

• Peak detection in spectral data within a configurable m/z tolerance (ppm or absolute)
• Offline lock mass recalibration using up to 5 reference ions per MS level
• Gaussian peak fitting for accurate estimation of fitted m/z values, FWHM, and fit quality (R²)
• Targetlist processing with optional lock mass recalibration correction
• MS2/MS3 support with precursor m/z directory matching and collision-energy parsing
• Gap analysis (min/max/mean/median m/z gaps) for data quality assessment
• Save and load configurations per tab (presets.lxx)
• Cross-platform (Windows, macOS, Linux)

Requirements

• Python >= 3.11

PySide6, pandas, numpy, and scipy are installed automatically as dependencies.

Installation

pip install alex123-extractor

Usage

Run the application:

alex123-extractor

Or via the Python module:

python -m alex123_xtractor

Then, in the app:

1. Select the target directory -- where targetlist_ms*.txt and output files live. Presets are loaded automatically if a presets.lxx is present.
2. Select the spectral directory -- the folder with the spectral .txt files.
3. Switch to the MS1, MS2, or MS3 tab.
4. Configure lock mass ions (optional) -- reference m/z values and their tolerance/offset settings.
5. Click "Check calibration" to run offline lock mass recalibration; gap analysis runs automatically afterwards.
6. Set the general search tolerance and offset, then click "Search" -- or press F8 -- to process the target list.

F8 always starts the search of the tab you are currently on. While a search is running the button is disabled, so a second press cannot start it twice.

Input Files

Output Files

Written to the target directory:

License

alex123-extractor 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.