ELIXIR resource bio. tools can be accessed via the link: https://bio.tools/t?page=1&q=proteomics&sort=score.
MegaGo: Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets (https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00926)
MegaGO is available as a web application at https://megago.ugent.be 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 https://github.com/MEGA-GO/.
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers (https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00904)
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, https://github.com/OpenMS/OpenMS and https://www.openms.de/)
Ultra-fast MS1/MS2 deconvolution for Top-Down Proteomics (https://doi.org/10.1016/j.cels.2020.01.003, https://www.openms.de/comp/flashdeconv/ )