Add High Res MS and Low Res MS presets for Comet adapter

[t0mdavid-m]

Summary

Added two new instrument-specific presets to optimize Comet adapter configuration for different mass spectrometry resolution types.

Changes

• High Res MS preset: Optimized for high-resolution MS2 instruments (Orbitrap, TOF)

  • Sets instrument type to high_res
  • Configures fragment mass tolerance to 0.015 ppm
  • Sets fragment bin offset to 0.0

• Low Res MS preset: Optimized for low-resolution MS2 instruments (Ion trap)

  • Sets instrument type to low_res
  • Configures fragment mass tolerance to 0.50025 ppm
  • Sets fragment bin offset to 0.4

Details

These presets provide sensible defaults for users working with different mass spectrometry instruments, eliminating the need for manual configuration of instrument-specific parameters. The fragment mass tolerance and bin offset values are calibrated for each instrument class to balance sensitivity and specificity.

https://claude.ai/code/session_01B8uy8fQnZ9q2tRsCiLuTev

Summary by CodeRabbit

• New Features

  • Added two new specialized presets for mass spectrometry analysis: "High Res MS" optimized for high-resolution instruments and "Low Res MS" optimized for low-resolution instruments and ion traps.

• Chores

  • Removed three deprecated presets ("High Specificity", "Fast Analysis", and "Metabolomics Default") to simplify preset selection and focus on key workflows.

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[coderabbitai]

Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

The presets.json file was restructured to replace "High Sensitivity" with "High Res MS" and introduce "Low Res MS", while removing "High Specificity", "Fast Analysis", and "Metabolomics Default" presets and their nested parameter blocks.

Changes

Cohort / File(s)	Summary
Preset Configuration Update presets.json	Replaced "High Sensitivity" preset with "High Res MS" (CometAdapter, high_res instrument, fragment_mass_tolerance 0.015); added new "Low Res MS" preset (CometAdapter, low_res instrument, fragment_mass_tolerance 0.50025); removed "High Specificity", "Fast Analysis", and "Metabolomics Default" presets along with their multi-block FeatureFinderMetabo and FeatureLinkerUnlabeledKD parameter trees.

Poem

🐰 Presets hop and skip with care,
High Res and Low Res now in pair,
Old branches trimmed, the tree's more neat,
Mass tolerance finds rhythm sweet!

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