This Java tool is used to convert clustering results into a different file format. It's most important feature is that consensus spectra can be converted into the MSP file format. Thereby, a spectral library can quickly be created based on the clustering results.
- Download the latest ZIP file from the release section
- Extract the ZIP file
- Launch the tool using
java -jar clustering-file-converter-[VERSION].jar
where[VERSION]
will vary depending on the release.
The complete list of options is shown using the -help
parameter.
The basic conversion to an MSP file looks like this:
java -jar clustering-file-converter-1.0-SNAPSHOT.jar \
-format msp \
-output_path my_library.msp \
-min_ratio 0.7 \
-min_size 3 \
-spec_lib_add_annotation \
my_cluster_result.clustering
This will convert the my_cluster_resul.clustering
clustering result
file into one MSP file.
Only clusters where 70% of the spectra were identified as the same
peptide (-min_ration 0.7
) with at least 3 spetra (-min_size 3
)
will be included in the MSP file.
The addition of annotations (-spec_lib_add_annotation
) is optional
but is required by some downstream tools.