clustering-file-converter

Introduction

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.

Installation

1. Download the latest ZIP file from the release section
2. Extract the ZIP file
3. Launch the tool using java -jar clustering-file-converter-[VERSION].jar where [VERSION] will vary depending on the release.

Usage

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.