// job selection -------------

job.auto_make_files = true
job.merge_adduct_ini = true
job.alignment = true
job.alignment.new_alignment_calc = true
job.alignment.revision_alignments = true
job.alignment.check_neighbor_alignments = true
job.alignment.check_isotope_alignments = true
job.alignment.check_34S_peaks = true
job.flavonoid_search = true
job.database_search = true
job.output_aligned_file_simple = true

// alignment settings -------------

alignment.method = 1
alignment.mode_rt = fwhm
alignment.method_regression = false
alignment.output_type = ids
alignment.method_both_best_match = true
alignment.margin_rt_ref = 5.0
alignment.margin_rt_target = 5.0
alignment.margin_mass_resolution_high = 5.0
alignment.margin_mass_resolution_low = 15.0
alignment.factor_fwhm = 3.0
alignment.min_fwhm = 3.0
alignment.max_fwhm = 15.0

restore_unused_peaks.margin_rt_sec_find_dif_rt = 30.0
restore_unused_peaks.margin_rt_sec_find_unused_peak = 30.0
restore_unused_peaks.margin_mass_ppm_find_unused_peak = 10.0
restore_unused_peaks.margin_rt_sec_find_used_peak = 10.0
restore_unused_peaks.margin_mass_ppm_find_used_peak = 5.0

find_best_msn.cleanup.round_decimal_fragment = 1
find_best_msn.cleanup.round_decimal_precursor = 1
find_best_msn.cleanup.cutoff_intensity_ratio = 0.05
find_best_msn.cleanup.cutoff_intensity_absolute = 500.0
find_best_msn.cleanup.num_top_ions = 50
find_best_msn.grouping.limit_ratio_group_member = 0.5
find_best_msn.grouping.limit_ratio_base_peak_intensity = 0.5

find_best_msn.matcher.add_new = 0.9, 0.2
find_best_msn.matcher.add = 0.7, 1.0E-4
find_best_msn.matcher.add = 0.8, 0.001

find_best_msn.ms_level_to_top_ions.add_new = 3, 4

find_best_msn.filter_info.add_new = 1, FTMS
find_best_msn.filter_info.add = 2, ITMS
find_best_msn.filter_info.add = 3, ITMS

// settings for checking neighbor alignments -------------

check_neighbor_alignments.margin_rt_sec = 30.0
check_neighbor_alignments.margin_mass_ppm = 5.0

// settings for chekcing isotope alignments -------------

check_isotope_alignments.margin_rt_sec = 90.0
check_isotope_alignments.margin_mass_ppm = 5.0
check_isotope_alignments.max_repeat_num = 1
check_isotope_alignments.max_charge = 6
check_isotope_alignments.fwhm_factor = 3.0
check_isotope_alignments.fwhm_min_sec = 3.0
check_isotope_alignments.fwhm_max_sec = 15.0
check_isotope_alignments.limit_overlap_rate = 0.1

// settings for checking 34S peaks -------------

check_34S_peaks.margin_rt_sec = 20.0
check_34S_peaks.margin_mass_ppm = 3.0

// settings for database search -------------

database_search.margin_mass = 20.0
database_search.margin_is_ppm = true
