Over the last few years, mass spectrometry (MS) studies of the proteome and peptidome have increased exponentially in numbers and also in complexity. To gather insight into the underlying biology, researchers often rely on historically grown platforms that suffer from complexities requiring developer guidance to use. Additionally, some researchers manually string together multiple single-task tools or even fewer create custom pipelines, requiring programming knowledge. Challenges with data management between analysis steps, sharing of the used parameters, replicability of the analyses across large dataset cohorts, and general accessibility are a result.

To address these challenges, a user-friendly tool that provides a one-stop-shop for downstream proteomic and peptidomic analysis in an easy-to-use graphical interface is required. Here, we introduce an open-source tool named PROTzilla in response. Our intuitive tool offers flexibility to customize data processing, ensures the storage of applied parameters for reproducible sharing of analysis workflows, and enables automated analysis through a command line interface for large-scale studies.

PROTzilla comprises a Python package with preprocessing, analysis, high-quality plotting capabilities, and integration of external knowledge bases alongside a user-friendly and browser-based interface. Besides proteomic and peptidomic analysis workflows, PROTzilla also provides analysis methods for post-translational modification (PTM) centric research questions. Furthermore, our tool, for the first time, enables the direct continued analysis of proteins of interest and their associated peptides and PTMs, including a graph-based sequence coverage model for different isoforms. Utilizing our cross-platform tool PROTzilla researchers can effortlessly perform analysis tasks and generate publication-ready visualizations, eliminating the need for programming knowledge. The sharable analysis workflows in PROTzilla are reproducible as well as automatable and community members can easily contribute new functionality.

With PROTzilla, we aim to simplify proteomics and peptidomics analysis in the field though enhanced flexibility, transparency, and reproducibility of analysis and reporting. We anticipate that this open-source tool will help researchers to effectively generate knowledge from their proteomics and peptidomics experiments and improve current practices for analysis sharing and reporting.