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Document current limitations and assumptions in the README #9

Description

@eneskemalergin

Summary

The repository currently describes the method, but it does not clearly list the assumptions and current limits of the implementation.

Tasks

  • add a limitations section to the README
  • mention the current UniMod assumption
  • mention supported source formats and any source-specific heuristics

Acceptance criteria

  • readers can quickly see what is supported today
  • readers can quickly see what is not supported yet

Why this matters

Clear limits reduce misuse and support questions.

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documentationImprovements or additions to documentationgood first issueGood for newcomers

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