DXMSMS.exe program looks for matches of crosslink masses for given protein sequences, stored in 
DXMSMS_Mass.txt and 
DXMSMS_Sequences.txt files, respectively.
Matches can be restricted by several peptides conditions, which are defined in the file 
DXMSMS_Controls.txt, as well as, by CL-containing, CL-noncontaining b- and y- fragment masses and at least by one cleavage product mass which are stored in 
DXMSMS_DX_Fragments.txt, 
DXMSMS_Fragments.txt and 
DXMSMS_Cleavage_Products.txt, respectively.
Results are saved in the file 
DXMSMS_Search_Results.txt
All files should be in the same directory.
Program works iteratively.
Control and input values can be changed and saved in corresponding files before each prompt.
Most convinient way of using the program is to keep program window running with control and input files opened on a desktop with Notepad.
Input values and control parameters can be changed in each corresponding text file window and can be saved with Ctrl+S key combination before each run.
Run then can be initiated by pressing "Enter" key in the program window.


Description of the program controls saved in DXMSMS_Controls.txt file:
BiPS    CL: DSS EGS DTSP BiPS DNBDPS TEABS EDC		- crosslinking reagent name (need to be followed by space);
0.3  	Mass tolerance, Da				- crosslink mass tolerance;
0.3  	Fragment tolerance, Da				- MSMS fragment masses tolerance;
0.3  	Cleavage tolerance, Da				- cleavage products masses tolerance;
K YST     Crosslinking residue, 0-all			- amino acid residues which can be crosslinked, N-terminus is always included (need to be followed by space);
KR 	LIWFAYH   Digest, 0-all				- digest restrictions (need to be followed by space);
0       Present internal sequence, 0-all		- subsequence present in at least one of crosslinked peptides (need to be followed by space);
0    	Non-present internal amino acids, 0-all		- crosslinks containing listed aminoacids will be excluded from results (need to be followed by space);
0    	D at DX fragmentation position, 0/1		- results will be restricted only to those containing aspartic acid residue at the fragmentation position
							  corresponding to the value of isotopically-coded fragments saved in DXMSMS_DX_Fragments.txt file;
0    	Deadends and internal only, 0/1			- results will be restricted only to intra-peptides or dead-end crosslinks.


DXMSMS_Cleavage_Products.txt file need to be empty to avoid taking cleavage products into consideration.


Multiple sequences (up to 28) need to be separated by line containing ">" sign.