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MineXpert2 (of the http://www.msxpertsuite.org software collection) is a desktop-oriented program that allows one to visualize mass spectrometric data in their full MS^n depth. Sophisticated mouse-driven mass data integrations are easily performed. It is the continuation of mineXpert2, ported to the rewrittent libXpertMass and libXpertMassGui libraries.

PAPPSOms++ is a comprehensive C++ library including useful functions to handle mass spectrometric data, either in a proteomics setting or for data visualization. Abstractions include peptides, proteins, isotopic clusters, mass/drift spectra...

C++ implementation of SpecOMS and new developments

mechanistic-statistical environment

https://msegrp.pages-forge.inrae.fr/mse

GroupingProtein does filtering, protein inference and grouping of mass MS/MS identification result (thousands of samples, high resolution mass spectrometers)

R package for OpenFLUID

OpenFLUID framework and applications

i2MassChroQ (identification & inference -- mass chromatogram quantification) is the successor of X!TandemPipeline-Java. Following a full rewrite in C++17 and integration of the MassChroQ module, i2MassChroQ features a quantitative proteomics solution

Lightweight C++ and Java library to produce Open Document Spreadsheet (.ods) files. The main goal is to write data as simply as writing it to a simple text file (csv or tsv). Libodsstream allows yout to read and write ODS files as stream

A library that contains a subset of the ProteoWizard libpwiz library with code mainly aimed at loading MS files (XML-based and MGF).

Model to simulate the spread of Map within and between herds via trade movements between dairy herds. Some control measures can be applied. Model is mechanistic and data-driven, stochastic, discrete-time and individual-based.