Extensions for better usability of the cross-linking tool MaXLinker.
MaXLinker requires Python 3.7 (any of the 3.7.xx but not higher or lower than 3.7) and the extension script additionally require pandas and xlsxwriter.
- Install pandas:
pip install pandas - Install xlsxwriter:
pip install xlsxwriter
DESCRIPTION:
A script to re-format fasta files to be usable with MaXLinker.
USAGE:
maxlinkerFastaFormatter.py f [f ...]
[-o OUTPUT]
[-h]
[--version]
positional arguments:
f Fasta file to process, if second filename
is given it will be used as the output name!
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Name of the output file.
--version show program's version number and exit
Example usage:
python maxlinkerFastaFormatter.py human_proteome.fasta -o human_proteome_maxlinker.fasta
DESCRIPTION:
A script to group crosslinks from MaXLinker results files by sequence and position.
USAGE:
maxlinkerSeqAndPosGrouper.py f [f ...]
[-o OUTPUT]
[-xlmod CROSSLINKER_MODIFICATION]
[-h]
[--version]
positional arguments:
f MaXLinker result file to process, if second filename
is given it will be used as the output name!
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Name of the output file.
-xlmod CROSSLINKER_MODIFICATION, --crosslinker-modification CROSSLINKER_MODIFICATION
Residue that the Crosslinker binds to e.g. K for DSSO.
It's also possible to specify multiple residues e.g.
KSTY for DSSO if you want to consider all possible links
--version show program's version number and exit
Example Usage:
python maxlinkerSeqAndPosGrouper.py my_results_uniq.tsv -o results_grouped
MaXLinker to IMP-X-FDR converter
The main purpose of this script is to convert MaXLinker output files to MS Annika format - which are usable with the IMP-X-FDR tool. This way MaXLinker can be benchmarked on synthetic peptide libraries.
DESCRIPTION:
A script to convert MaXLinker *.tsv result files to MS Annika format as
Microsoft Excel worksheets for usage with IMP-X-FDR (v1.1.0).
USAGE:
maxlinkerToAnnikaResultConverter.py f [f ...]
[-o OUTPUT]
[-xl CROSSLINKER]
[-xlmod CROSSLINKER_MODIFICATION]
[-mod MODIFICATIONS]
[-h]
[--version]
positional arguments:
f MaXLinker result file to process, if second filename
is given it will be used as the output name!
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Name of the output file.
-xl CROSSLINKER, --crosslinker CROSSLINKER
Name of the Crosslinker e.g. DSSO.
-xlmod CROSSLINKER_MODIFICATION, --crosslinker-modification CROSSLINKER_MODIFICATION
Residue that the Crosslinker binds to e.g. K for DSSO.
It's also possible to specify multiple residues e.g.
KSTY for DSSO if you want to consider all possible links
-mod MODIFICATIONS, --modifications MODIFICATIONS
Modifications as dictionary string / in json format.
--version show program's version number and exit
Example Usage:
python maxlinkerToAnnikaResultConverter.py my_results_uniq.tsv -o my_results_converted -xl DSSO -xlmod KSTY -mod "{\"M\": \"Oxidation\", \"C\": \"Carbamidomethyl\"}"
If you are using one of the MaXLinker extension scripts please cite:
MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity
Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, and Viktoria Dorfer
Journal of Proteome Research 2023 22 (9), 3009-3021
DOI: 10.1021/acs.jproteome.3c00325