# Introduction

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  <img src="https://github.com/MannLabs/alphapeptstats/blob/main/alphastats/gui/alphapeptstats_logo.png?raw=true" />
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AlphaPeptStats is an open-source package for analyzing mass spectrometry-based proteomics data.

AlphaPeptStats was developed to simplify and standardize the process of analyzing complex datasets. Hereby AlphaPeptStats supports proteomics data generated by `AlphaPept`, `DIA-NN`, `FragPipe`, `MaxQuant` and `Spectronaut` and quantiative proteomics results in `mzTab` format. The tool allows a structured workflow from importing data, preprocessing data to visualization.

AlphaPeptStats was developed by the [Mann Group at the University of Copenhagen](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](../LICENSE.txt). External Python packages (available in the [requirements.txt](../requirements.txt) file) have their own licenses, which can be consulted on their respective websites.

The workflow consists of:
1. Import of proteomics data
2. Creation of the DataSet, consisting of the imported proteomics data and metadata
3. Data preprocessing (optional)
4. Statistical Analysis and Visualization