README

= Disulfide Searcher

This is a tool which provides a way to search a spectrum and determine which disulfide bridging explains the fragmentation pattern in intra-peptide disulfide bonds.It is compatible with single and double disulfide bonds (2-4 cysteine residues).   

= Publication
Ogawa N, Taylor RM, Woodbury DJ, Prince JT. Resolving double disulfide bond patterns in SNAP25B using liquid chromatography-ion trap mass spectrometry. J Mass Spectrom. 2013;48(6):660-668. 
https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.3211

==Instruction on use

1. Convert RAW file to mzML
2. Extract target MS/MS spectra from mzML file
3. Set Parameters
4. Execute cmdline.rb

== Note on Patches/Pull Requests
 
* Fork the project.
* Make your feature addition or bug fix.
* Add tests for it. This is important so I don't break it in a
  future version unintentionally.
* Commit, do not mess with rakefile, version, or history.
  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
* Send me a pull request. Bonus points for topic branches.

== Copyright

Copyright (c) 2010 Brigham Young University. See LICENSE for details.