MaXLinker Extensions

Extensions for better usability of the cross-linking tool MaXLinker.

Requirements

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

MaXLinker FASTA file converter

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

MaXLinker crosslink grouper

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\"}"

Citing

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

License

MIT License

Contact

[email protected]

hgb-bin-proteomics / maxlinker_extensions Goto Github PK