Helper scripts for crosslink analysis.
- Python 3.10+
- Packages as specified in requirements.txt:
pip install -r requirements.txt - Or what is specified in the specific sub-directories!
- 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
An example implementation of calculating the MS1 Error for CSMs from MS Annika.
See notebook here: ms1_error.ipynb
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.
Filters out duplicate proteins and proteins with ambiguous sequences (e.g. containing amino acid letter code "X") from a FASTA file
and writes a new FASTA file with suffix "_unique_seq_no_X.fasta".
More information: see here
Counts in how many mass spectra the specified m/z values appear (e.g. to find diagnostic ions). Mass spectra should be given
in .mgf format. Masses should be given in a single .txt file with one mass per line. The script simply matches the masses
to the m/z array of every mass spectrum. No deisotoping or deconvolution is performed.
More information: see here
If you are using scripts of this repository please cite MS Annika.