FLASHApp/presets.json at develop · OpenMS/FLASHApp · GitHub

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{
    "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 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
            }
        }
    }
}