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R script used for peak calling on the benchmarking dataset as in Dumolin et al. 2019.


Rscript peak_calling_cwt.R FullMS_directory

where FullMS_directory is the name of a directory containing .txt files of quality filtered, raw mass spectra. Each text file should have two tab-spearated columns without headers. First column is the m/z value and second column the intensity value as in the example below:

#m/z int
1998.75 686
1999.17 603
1999.59 640
2000.00 599

Output is stored in the PKL4DICE directory. The directory contains the peak lists for each spectrum as called by the MassSpectWavelet package (1 file per spectrum).


  • Rscript version 3.4.4 or newer (not tested on older versions)
  • MassSpecWavelet package version 1.48.1, available from Bioconductor (Du et al. 2006)

References: Du P, Kibbe WA, Lin SM (2006). “Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.” Bioinformatics, 22, 2059-2065.

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