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Software

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

XlinkX/PD

Intuitive data analysis pipeline for crosslinking mass spectrometry data.

Features:

  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.

XMAS/ChimeraX

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

Features:

  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.
User interface for FragmentLab, showcasing the different options.

FragmentLab

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

Features

  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.