The current documentation for X! TANDEM is in the form of a set of UML diagrams illustrating how the various algorithms in X! TANDEM work in detail. For all other details, please see the documentation in the source code.

1. A state diagram showing how X! TANDEM works.
2. An activity diagram of the how information is loaded.
3. An activity diagram of how scoring is done.
4. A state diagram of the scoring mechanism.
5. A state diagram of how peptide sequences are created from protein sequences.
6. A state diagram of how protein sequences are loaded from a file.
7. A state diagram of how spectra are evaluated by peptide mass.
8. A class diagram of the loadmspectrum class.
9. A class diagram of the mprocess class.
10. A class diagram of the mreport class.
11. A class diagram of the mscore class.
12. A class diagram of the msequence class.
13. A class diagram of the mspectrum class.

Is there something you would like to see included, or documentation that you would like to contribute? Please let use know - contact@thegpm.org.