Computational Proteomics Tools

Generic Computational Tools

ELIXIR resource bio. tools can be accessed via the link:

EPIC-XS Funded Computational Tools

MegaGo: Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets (

MegaGO is available as a web application at and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the MIT license and is available at

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers (

The BioContainers Registry provides a fast and convenient way to find and retrieve bioinformatics tool packages and containers.

QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories


OpenMS framework for computational mass spectrometry

OpenMS offers an open-source software C++ library (+ python bindings) for MS data analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS and Linux. (doi:10.1038/nmeth.3959, and


Ultra-fast MS1/MS2 deconvolution for Top-Down Proteomics (, )