The ScheltemaLAB creates powerful software for the analysis of mass spectrometry data and placing the results back in a structural context.


Intuitive data analysis pipeline for crosslinking mass spectrometry data.


  1. 1. Define any reagent;
  2. 2. Supports all acquisition strategies;
  3. 3. Multi-level FDR control;
  4. 4. Connects well with others through data standards.


Powerful protein structure editing/modeling supported with crosslinking mass spectrometry data. Plays very well with protein-protein docking software DisVis/HADDOCK.


  1. 1. Load the output of many XLMS search engines;
  2. 2. Map and visualize crosslinks on protein structures;
  3. 3. Easily filter crosslinks on replicates / DisVis results;
  4. 4. Easily trigger protein-protein docking in HADDOCK.


Visualization of peptide fragmentation spectra and data analysis to extract new features that can be used for identification.


  1. 1. Loads PD, MQ and FragPipe outputs;
  2. 2. Annotation of fragmentation spectra;
  3. 3. Unbiased search of novel fragment ions;
  4. 4. Peptide coverage maps;
  5. 5. Load and compare fragmentation spectrum predictions.