DXDXSet program searches for mass matches between uncleaved and cleaved DX masses according to the cleavage mass losses for dead-end, intra- and inter-peptide crosslinks in a set of multiple spectra combined into total files.
Uncleaved DX, Cleaved DX and Cleavage mass loss values must be stored in DXDX_Controls.txt file and occupy top three lines. 
Fourth line contains tolerance value in Daltons.
DXDXSet.exe is designed for using of DXSet.exe Total_.txt mass list files as input files. 
Both files for uncleaved and cleaved sets should contain the same number of spectra in similar order (e.g. fifth mass list from cleaved sample spectrum should correspond to fifth mass list from uncleaved spectrum etc.).
Uncleaved and cleaved total mass lists values must be stored as two columns of values in .txt file as output format of DXSet.exe program Total _.txt: 
first column of masses occupies 10 characters, followed by TAB and by four characters of spotname.
Input file names do not require neither directory root or extensions.
All files should be in the same directory as the program file.
Copy of the screen output will be stored in DXDXSet_Results.txt file.