SYSTEM REQUIREMENTS FOR LINUX (UNIX based systems)
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	* Perl 5.10 and above

	* GNU C++ compiler (g++)

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INSTALLATION AND USAGE ON LINUX
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	* Extract the downloaded file from the command line:
             tar -zxvf DisConnect.tar.gz

	* cd DisConnect_Linux

	* sh run.sh

	* Key in the inputs as prompted    
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INPUT/OUTPUT OPTIONS FOR LINUX
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Enter 1 / 2 if you are assigning proteolytic or MS2/n fragment ions respectively

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>> If 1 is chosen at this stage (i.e., assignment of MS data for proteolytic fragments) >>
Before Starting: 
	# Paste the protein sequence, ending with a * symbol, in the file "prot_seq"
	# Put the m/z values, in the format 'm/z value'space'charge state' (e.g. 1020.2 3, where the m/z value 
        is 1020.2 and charge state 3)in the file 'peak_mass_ms'

	1. Enter the name/symbol for the protein of interest

	2. Enter 1 / 2 for monoisotopic / average mass

	3. Enter 1 / 2 if the protein C-terminus is Amidated / Non-amidated

	4. Enter your choice of proteases

	Enter 1 for Trypsin
	Enter 2 for Trypsin-P
	Enter 3 for V8(DE)
	Enter 4 for V8(D)
	Enter 5 for Asp-N
	Enter 6 for Lys-C
	Enter 7 for Arg-C
	Enter 8 for CNBr
	Enter 10 for user defined protease

	5. Enter the number of additional proteases to be used

	6. Enter the number of allowed proteolytic miscleavages (1-3; upto three miscleavages allowed)

	7. Enter window range for match with MS data depending on the resolution of the experimental setup.

	8. Results will be stored in the path ./Results_MS in the format "match_MS_protein name/symbol"  within the DisConnect_Linux folder. 
           Also a file named "inp_MSn_match_MS_protein_name.out" will be provided for input to subsequent MSn experiments for each MS 
	   fragment ion.

********************************************************************

>> If 2 is chosen at this stage (i.e., assignment of MS2/n data) >>
#Before Starting: 
	# Put the m/z values of the fragment ions, in the format 'm/z value'space'charge state' (e.g. 1020.2 3, where the 
	  m/z value is 1020.2 and charge state 3)in the file 'peak_mass_ms2' (for MS2) or 'peak_mass_msn' (for MSn)

	1. Enter 1 / 2 for monoisotopic / average mass

	2. Enter 1 / 2 if you are calculating on whole sequence (MS2) / daughter fragments (MSn; n>2)

		If Step 2 = (1) ---> Enter the complete polypeptide sequence: 	(Polypeptide sequence can be entered using 
										the standard one letter codes. For peptide 
										containing multiple chains, like insulin, 
										a letter X should be entered between the two 
										chains(e.g If a peptide conatins two 
										polypeptide chains with sequence GVCSF and 
										RLTCY then the input is GVCSFXRLTCY). For 
										user benefit, if these peptides are results 
										of proteolytic digestion then an input file 
										in the Result_MS folder is created, named 
										"inp_MSn_match_MS_protein name.out", that 
										conatins the peptide sequence in the required 
										format for the MS2 analysis. The user can copy 
										the respective sequence from there and paste it) 																																					   

		If Step 2 = (2) ---> Enter the complete polypeptide sequence: (As above)
                     		     Enter the fragment polypeptide sequence:	(Format for this input sequence is given 
										inside the Resut_MSn folder, termed as
 										inp_Result_MSn_rigorous/smart_Entered complete/
										fragment sequence. This is obtained during the
										the structure determination of the parent ion from
										the preceeding stage of MS/MS ions. 
										Copy the corresponding structure of the ion 
										undergoing MSn fragmentation from this file).

	3. Enter 1 / 2 for smart / rigorous mode of calculation (Smart mode considers only the Cys residue mass values 
								of 135 & 69 Da, and rigorous considers all the four 
								possible values of 101, 103, 135, 69. Users are advised 
								to use Smart mode for posstiive ion CID fragmentation, 
								as it is the prevalent mode of fragmentation under this 
								condition).

	4. Enter the mass error tolerance based on the resolution of the experimantal setup

	5. Enter 1/2/3/4/5 for normal peptide fragments/fragments with CO loss/fragments with H2O loss/fragments with NH3 loss/fragments with NH3+CO loss
	
	6. Depending on the number of C-termini in the sequence (say x) the code will ask for the amidated(enter 16) / non-amidated(enter 17) status for each C-term
	   
	   Enter mass to be added for C-term 1 status
	   .
	   .
	   .
	   Enter mass to be added for C-term x status

	7. Enter 1/2 for ion trap/ no ion trap filtering 
	
	8. Results will be stored in the path ./Results_MSn in the format "Result_MS2/n_smart/rigorous_Entered complete/fragment sequence/results.out"  
	   within the DisConnect_Linux folder.

	9. For MSn experiments, the input parent fragment ion structure needs to be inserted twice. 
	   
	   (a)		At first, at Step 2(2) stage. Here the input ion has to retain a numbering scheme (which has been removed from the 
	   final output for the clarity of presentation) for technical purposes. An output file named "inp_Result_MSn_smart/rigorous_Entered complete/
	   fragment sequence" is also given within the Results_MSn folder, retaining this numbering scheme for the fragment ions. 
	   For any MSn experiments, the input of the corresponding parent ion structure should be taken from this output file. 
	   It is to be noted that this file contains all the ion structures, without ion trap filtering. The user need
	   to select the corresponding numbered structure of the ion shown in the result file "Result_*".

	   (b) 		Next, it needs to be inserted again after Step 7. Here, the Input should be in the output fromat and thus can directly be copied from the 
	   MS2 output file, termed as "Result_MS2/n_smart/rigorous_Entered complete/fragment sequence/results.out". 
		


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All the benchmark data discussed in text are given the folder ./benchmark-data

For more details refer to the Methods in the Documentation folder and the reference given below. The program package DisConnect is distributed under the BSD License (see License.txt).

If you are using this package, please also refer to (Rapid Mass Spectrometric Determination of Disulfide Connectivity in Peptides and Proteins. Bhattacharyya M, Gupta K, Gowd KH, Balaram P , Mol. BioSyst.,2013,XX,XX-XX)

Please contact the following in case of any difficulties:

moitrayeebhattacharyya@gmail.com
talkingtothekg@gmail.com

Thank you for using DisConnect !!!




