Tool to get peptide-pairs from MS-GFDB results.

1. Usage: java -jar peptpair.jar

                          -i msgfdb_results_file [*.tsv format]

                          -o output_file [If not specified, it is automatically generated, (*.pairs)]

                          -score_cut msgf_score [to consider only PSMs more than the specified score. Default: all PSMs]

                          -ignore_cs [If this option is used, charge states between are ignored. Default: PSMs with same charge states are regards as pairs]

2. Output: (tab-separated)

 - Columns: overlap   spec1   pept1   cs1   msgfscore1   specprob1   spec2   pept2   cs2   msgfscore2   specprob2

3. Example: java -jar peptpair.jar -i msgfdb.tsv

               java -jar peptpair.jar -i msgfdb.tsv -score_cut 10 -ignore_cs

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  1. Feb 22, 2014

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