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 and is freely available with an Apache License. External Python packages (available in the requirements folder) have their own licenses, which can be consulted on their respective websites.
The workflow consists of:
Import of proteomics data
Creation of the DataSet, consisting of the imported proteomics data and metadata
Data preprocessing (optional)
Statistical Analysis and Visualization