massxpert

polymer chemistry modelling and mass spectrometry data simulation (runtime)
  http://www.msxpertsuite.org/
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MassXpert allows the user to perform the following tasks:

- Make brand new polymer chemistry definitions; - Use the definitions to easily perform calculations in a desktop calculator-like manner; - Perform sophisticated polymer sequence editing and simulations; - Perform m/z list comparisons;

Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches...

This package ships the massXpert program.