ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.
UniDec is described in "Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles" by Michael T. Marty , Andrew J. Baldwin , Erik G. Marklund , Georg K. A. Hochberg , Justin L. P. Benesch , and Carol V. Robinson, Analytical Chemistry, 2015, DOI: 10.1021/acs.analchem.5b00140.
Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics (more about its history). It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.