diff --git a/presets.json b/presets.json index 1099493..d1878af 100644 --- a/presets.json +++ b/presets.json @@ -1,44 +1,19 @@ { "topp-workflow": { - "High Sensitivity": { - "_description": "Optimized for detecting low-abundance features with higher noise tolerance", - "FeatureFinderMetabo": { - "algorithm:common:noise_threshold_int": 500.0, - "algorithm:common:chrom_peak_snr": 2.0, - "algorithm:mtd:mass_error_ppm": 15.0 + "High Res MS": { + "_description": "Optimized for high-resolution MS2 (Orbitrap, TOF) when using ppm fragment tolerance", + "CometAdapter": { + "instrument": "high_res", + "fragment_mass_tolerance": 0.015, + "fragment_bin_offset": 0.0 } }, - "High Specificity": { - "_description": "Strict parameters for high-confidence feature detection", - "FeatureFinderMetabo": { - "algorithm:common:noise_threshold_int": 5000.0, - "algorithm:common:chrom_peak_snr": 5.0, - "algorithm:mtd:mass_error_ppm": 5.0 - } - }, - "Fast Analysis": { - "_description": "Faster processing with relaxed parameters for quick exploration", - "FeatureFinderMetabo": { - "algorithm:common:noise_threshold_int": 2000.0, - "algorithm:ffm:isotope_filtering_model": "none" - }, - "FeatureLinkerUnlabeledKD": { - "algorithm:link:rt_tol": 60.0, - "algorithm:link:mz_tol": 15.0 - } - }, - "Metabolomics Default": { - "_description": "Balanced parameters for general metabolomics analysis", - "FeatureFinderMetabo": { - "algorithm:common:noise_threshold_int": 1000.0, - "algorithm:common:chrom_peak_snr": 3.0, - "algorithm:mtd:mass_error_ppm": 10.0, - "algorithm:ffm:charge_lower_bound": 1, - "algorithm:ffm:charge_upper_bound": 3 - }, - "FeatureLinkerUnlabeledKD": { - "algorithm:link:rt_tol": 30.0, - "algorithm:link:mz_tol": 10.0 + "Low Res MS": { + "_description": "Optimized for low-resolution MS2 (Ion trap) when using ppm fragment tolerance", + "CometAdapter": { + "instrument": "low_res", + "fragment_mass_tolerance": 0.50025, + "fragment_bin_offset": 0.4 } } }