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

Voytik, Eugenia; Bludau, Isabell; Willems, Sander; Hansen, Fynn; Brunner, Andreas-David; Strauss, Maximilian T.; Mann, Matthias

Summary 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 prior 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.