Crosslink Utils

Helper scripts for crosslink analysis.

Requirements

• Python 3.10+
• Packages as specified in requirements.txt: pip install -r requirements.txt
• Or what is specified in the specific sub-directories!

find_shortest.py

• Finds the shortest cross-linked residue pair per crosslink in a mulitmeric structure of proteins with equal sequences.
• A detailed description of the script parameters is given in the script.
• Example usage:

  python find_shortest.py data/pyXlinkViewer_export.py -c AB,CD -t 27.0
  

MS Annika MS1 Error

An example implementation of calculating the MS1 Error for CSMs from MS Annika.

See notebook here: ms1_error.ipynb

Proteome Discoverer Result File Reader

Automatically read in results from a Proteome Discoverer study and combine metrics into a single table. In this example illustrated by reading numbers of peptide spectrum matches, crosslink spectrum matches and crosslinks.

• Jupyter notebook: see here
• Python script: see here
• R script (minimal): see here

Citing

If you are using scripts of this repository please cite MS Annika.

License

• MIT

Contact

[email protected]