ReCom is a modified version of the Comet project for the thorough analysis of post-translational modifications, developed at the Cardiovascular Proteomics laboratory at CNIC (Spain).
The .params file for ReCom includes several new parameters:
use_delta_closest: 0=no (default), 1=yes. Setting this to 1 will enable ReCom, setting this to 0 will perform a normal Comet-PTM search.deltamass_peaks: This is the path to the txt file containing the list of theoretical deltamasses.deltamass_peaks_tolerance: This is the tolerance in Da for matching experimental deltamasses to the list (default 1, will search for theoretical deltamasses within ±1 Da of the experimental deltamass.cand_number: This is the number of candidates to rescore for each identification (default 1)use_xcorr_corr: 0=no (default), 1=yes. Setting this to 1 will calculate the Corrected Xcorr value and use it to sort candidates and choose between experimental or theoretical. Regular Xcorr will still be calculated but not used for sorting.