AlphaMap: An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge [article]

Eugenia Voytik, Isabell Bludau, Sander Willems, Fynn Hansen, Andreas-David Brunner, Maximilian T Strauss, Matthias Mann
2021 bioRxiv   pre-print
Integrating experimental information across proteomic datasets with the wealth of publicly available sequence annotations is a crucial part in many proteomic studies that currently lacks an automated analysis platform. Here we present AlphaMap, a Python package that facilitates the visual exploration of peptide-level proteomics data. Identified peptides and post-translational modifications in proteomic datasets are mapped to their corresponding protein sequence and visualized together with
more » ... knowledge from UniProt and with expected proteolytic cleavage sites. The functionality of AlphaMap can be accessed via an intuitive graphical user interface or - more flexibly - as a Python package that allows its integration into common analysis workflows for data visualization. AlphaMap produces publication-quality illustrations and can easily be customized to address a given research question. Availability and implementation: AlphaMap is implemented in Python and released under an Apache license. The source code and one-click installers are freely available at https://github.com/MannLabs/alphamap. Supplementary information: A detailed user guide for AlphaMap is provided as supplementary data.
doi:10.1101/2021.07.30.454433 fatcat:ed5a6754urdtbcsyrxxbnd6qde