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Updated ion type definitions, output information, and batch mode
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Updated ion type definitions. User can now select CID or ECD (it will make sure the correct ion types are used). Other electron-based fragmentation chemistries will be added upon user request.
For internal fragment searches, output now contains mass resolution used to generate theoretical isotope envelopes and tolerance error for matches.
Batch mode is now available for internal fragments (several searches can be run automatically).