ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based proteomics data

Abstract Mass spectrometry-based proteomics generates increasingly large datasets requiring rapid quality control (QC) and preliminary analysis. Current software solutions often require specialized knowledge, limiting their routine use. We developed ProteoGyver (PG), an accessible, lightweight software solution designed for rapid QC and preliminary proteomics data analysis. PG provides automated QC metrics, intuitive graphical reports, and streamlined workflows for whole-proteome and interactomics datasets, significantly lowering the barrier to regular QC practices. The platform includes additional tools such as MS Inspector for longitudinal chromatogram inspection and Colocalizer for microscopy data. PG is easily deployed as a Docker container or standalone Python installation. PG is open-source and freely available in dockerhub and source code in github at github.com/varjolab/Proteogyver. Availability and implementation PG image and source code are available in github and dockerhub under LGPL-2.1.