xcorr_py is a Python implementation of the Comet cross-correlation score.

• xcorr_py generates the exact same xcorr scores as Comet 2025.02.0 and presumably earlier/later versions.

• Another independent Python xcorr implementation by M. Maccoss is available here with pyXcorrDIA.

• This is just a example program. Modified residues and higher charged fragments have not yet been implemented but are easy to do by extending calculate_fragment_ion_bins() to generate the proper set of fragment_ion_bins_uniq. I'm happy to add that support in if helpful to anyone.

• Lines 14, 15, and 16 is where you set the fragment parameters such as fragment_bin_width, fragment_bin_offset, and use_flanking_peaks (aka theoretical_fragment_ions in Comet). Low res and high res fragment ion settings, with and without flanking peaks, have been tested and confirmed to match Comet.

• The "test" directory contains the same spectra data and peptides for a Comet search as are encoded in xcorr_py.