java for proteomics

https://github.com/msdk mass spectrometry development kit (a library of algorithms).

https://github.com/wolski/PIPI - PTM invariant search

https://github.com/PRIDE-Utilities
https://github.com/compomics
https://github.com/PGB-LIV/mzidlib

Sebastian Boeckers group is developing Mass spectrometry software mostly in java:
https://bio.informatik.uni-jena.de/software/



BTW, there is more than CRAN and Bioconductor for R:
https://ropensci.org/