Skip to contents (site navigation)

MS Tools

H/D Exchange Calculator
Calculates number of exchangeable hydrogens, monoisotopic and average masses and displays a simple peptide statistics (example result)
H/D Experiment Planner
Creates a time schedule for H/D exchange experiments (example result)
Draw Map
Creates a graphical representation of protein sequence coverage (example result)
Draw H/D Heat Map
Draws graphical representation of H/D exchange using color gradients (heat maps) (example result)
Draw H/D Protection Plot
Creates a protection plot based on data from H/D exchange and allows comparison of various conditions (example result)
JMol Scripter
Visualization of H/D data on protein structure using JMol.
Draw H/D Exchange plots
Draws graphical representation of H/D exchange using plots

If you are using MS Tools use this citation in your papers please:
Kavan, D. and Man, P. "MSTools - Web based application for visualization and presentation of HXMS data" Int. J. Mass Spectrom. 2011, 302: 53-58.

You can also use the mirror at - Northern America.

If you have any questions, please do not hesitate to contact us at: or

H/D related sites worth visiting

Software from our laboratory

A PHP script suite to help to evaluate the MS/MS data of cyclic nonribosomal and ribosomal peptides.
A novel approach of high-accuracy FTICR-MS data utilization in protein quantification experiments.
Program mMass presents an open source multi-platform package of simple tools for mass spectrometric data analysis. It consist of several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks.

If you have any questions, please do not hesitate to contact Martin Strohalm.

A stand-alone, cross-platform and open-source de novo engine for identification of nonribosomal peptides (linear, cyclic, branched and branch-cyclic) from accurate product ion spectra.