We developed an open-access Python-based software tool available either as a downloadable library or web-based GUI. The pipeline simplifies the extraction and calculation of (absolute) protein abundances from unprocessed proteomics data, accommodating a range of experimental approaches based on label-free quantification. Our tool was conceived as a versatile and robust pipeline designed to ease and simplify data analysis, thereby improving reproducibility between researchers and institutions. Moreover, the robust modular structure of Alpaca allows its integration with other software tools.

Resources and Further Reading:

•  Alpaca GUI: https://alpaca.nube.uni-greifswald.de

•  Video Tutorial: https://grypstube.uni-greifswald.de/w/xrmy6G55kbrjd3BFcLLSfG

•  Full documentation: https://borfebor.github.io/alpaca_proteomics/

•  GitHub repository (source code & example data): https://github.com/borfebor/alpaca_proteomics

•  Jupyter tutorial notebook: https://github.com/borfebor/alpaca_proteomics/blob/main/tutorial.ipynb

•  Questions or feedback? Contact us via GitHub Issues or email.