Metadata-Version: 2.4
Name: ms_qc_tools
Version: 0.1.2
Summary: Quality control tools for mass spectrometry data
Author-email: Pedrioli Patrick <pedrioli@gmail.com>
License: LICENSE
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.20.0
Requires-Dist: matplotlib>=3.4.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: seaborn>=0.11.0
Requires-Dist: scipy>=1.7.0
Requires-Dist: pymzxml>=0.1.3.2
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: build; extra == "dev"
Requires-Dist: twine; extra == "dev"
Requires-Dist: deptry; extra == "dev"
Requires-Dist: tox; extra == "dev"
Requires-Dist: pyright; extra == "dev"
Dynamic: license-file

# ms_qc_tools

A Python package for quality control (QC) of mass spectrometry (MS) data. It processes mzXML and PSM (peptide-spectrum match) files to compute a comprehensive set of metrics and generate visualizations, helping researchers monitor instrument performance and data quality.

## Features

- **Comprehensive metrics**:
  - Basic scan metrics (number of scans, empty scans, etc.)
  - Chromatographic metrics (peak width, retention time distribution)
  - TIC/BPI summaries and percentiles
  - MSn quality metrics (precursor intensity, charge state distribution)
  - Fragmentation efficiency
  - Timing and duty cycle analysis
  - Peptide-level metrics (length, charge, modifications, hydrophobicity)
  - Identification rates and calibration deltas
- **Multiple plots**:
  - TIC and BPI chromatograms
  - MS1 feature maps (density plots)
  - Precursor charge state distributions
  - Fragmentation efficiency plots
  - Peptide property distributions
  - Calibration delta plots
- **Database storage**: Save all metrics to a SQLite database for longitudinal tracking.
- **Flexible API**: Use as a Python library or via command-line interface.

## Installation

``` shell
pip install ms_qc_tools
```
