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FAIMS_DDA_LFQ.json
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FAIMS_DDA_LFQ.json
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{"# Workflow": " FAIMS_DDA_LFQ", "database.db-path": "C\\:\\\\Users\\\\tcoop\\\\Downloads\\\\FragPipe-jre-19.1\\\\fragpipe\\\\bin\\\\2023-01-20-decoys-reviewed-isoforms-contam-UP000005640.fas", "crystalc.run-crystalc": "false", "database.decoy-tag": "rev_", "diann.fragpipe.cmd-opts": "", "diann.library": "", "diann.q-value": "0.01", "diann.quantification-strategy": "3", "diann.run-dia-nn": "false", "diann.run-specific-protein-q-value": "false", "diann.unrelated-runs": "false", "diann.use-predicted-spectra": "true", "diaumpire.AdjustFragIntensity": "false", "diaumpire.BoostComplementaryIon": "false", "diaumpire.CorrThreshold": "", "diaumpire.DeltaApex": "", "diaumpire.ExportPrecursorPeak": "false", "diaumpire.Q1": "false", "diaumpire.Q2": "false", "diaumpire.Q3": "false", "diaumpire.RFmax": "", "diaumpire.RPmax": "", "diaumpire.RTOverlap": "", "diaumpire.SE.EstimateBG": "false", "diaumpire.SE.IsoPattern": "", "diaumpire.SE.MS1PPM": "", "diaumpire.SE.MS2PPM": "", "diaumpire.SE.MS2SN": "", "diaumpire.SE.MassDefectFilter": "false", "diaumpire.SE.MassDefectOffset": "", "diaumpire.SE.NoMissedScan": "", "diaumpire.SE.SN": "", "diaumpire.run-diaumpire": "false", "freequant.mz-tol": "10", "freequant.rt-tol": "0.4", "freequant.run-freequant": "false", "ionquant.excludemods": "", "ionquant.heavy": "", "ionquant.imtol": "0.05", "ionquant.ionfdr": "0.01", "ionquant.light": "", "ionquant.locprob": "0.75", "ionquant.maxlfq": "1", "ionquant.mbr": "1", "ionquant.mbrimtol": "0.05", "ionquant.mbrmincorr": "0", "ionquant.mbrrttol": "1", "ionquant.mbrtoprun": "10", "ionquant.medium": "", "ionquant.minfreq": "0", "ionquant.minions": "1", "ionquant.minisotopes": "1", "ionquant.minscans": "3", "ionquant.mztol": "10", "ionquant.normalization": "1", "ionquant.peptidefdr": "1", "ionquant.proteinfdr": "1", "ionquant.requantify": "1", "ionquant.rttol": "0.4", "ionquant.run-ionquant": "true", "ionquant.tp": "0", "ionquant.uniqueness": "0", "ionquant.use-labeling": "false", "ionquant.use-lfq": "true", "ionquant.writeindex": "0", "msbooster.predict-rt": "true", "msbooster.predict-spectra": "true", "msbooster.run-msbooster": "false", "msbooster.use-correlated-features": "false", "msfragger.Y_type_masses": "", "msfragger.activation_types": "all", "msfragger.add_topN_complementary": "0", "msfragger.allowed_missed_cleavage_1": "2", "msfragger.allowed_missed_cleavage_2": "2", "msfragger.calibrate_mass": "2", "msfragger.check_spectral_files": "true", "msfragger.clip_nTerm_M": "true", "msfragger.deisotope": "1", "msfragger.delta_mass_exclude_ranges": "(-1.5,3.5)", "msfragger.deneutralloss": "1", "msfragger.diagnostic_fragments": "", "msfragger.diagnostic_intensity_filter": "0", "msfragger.digest_max_length": "50", "msfragger.digest_min_length": "7", "msfragger.fragment_ion_series": "b,y", "msfragger.fragment_mass_tolerance": "20", "msfragger.fragment_mass_units": "1", "msfragger.intensity_transform": "0", "msfragger.ion_series_definitions": "", "msfragger.isotope_error": "0/1/2", "msfragger.labile_search_mode": "off", "msfragger.localize_delta_mass": "false", "msfragger.mass_diff_to_variable_mod": "0", "msfragger.mass_offsets": "0", "msfragger.max_fragment_charge": "2", "msfragger.max_variable_mods_combinations": "5000", "msfragger.max_variable_mods_per_peptide": "3", "msfragger.min_fragments_modelling": "2", "msfragger.min_matched_fragments": "4", "msfragger.min_sequence_matches": "2", "msfragger.minimum_peaks": "15", "msfragger.minimum_ratio": "0.01", "msfragger.misc.fragger.clear-mz-hi": "0", "msfragger.misc.fragger.clear-mz-lo": "0", "msfragger.misc.fragger.digest-mass-hi": "5000", "msfragger.misc.fragger.digest-mass-lo": "500", "msfragger.misc.fragger.enzyme-dropdown-1": "trypsin", "msfragger.misc.fragger.enzyme-dropdown-2": "trypsin", "msfragger.misc.fragger.precursor-charge-hi": "4", "msfragger.misc.fragger.precursor-charge-lo": "1", "msfragger.misc.fragger.remove-precursor-range-hi": "1.5", "msfragger.misc.fragger.remove-precursor-range-lo": "-1.5", "msfragger.misc.slice-db": "1", "msfragger.num_enzyme_termini": "2", "msfragger.output_format": "pepXML_pin", "msfragger.output_max_expect": "50", "msfragger.output_report_topN": "1", "msfragger.override_charge": "false", "msfragger.precursor_mass_lower": "-20", "msfragger.precursor_mass_mode": "selected", "msfragger.precursor_mass_units": "1", "msfragger.precursor_mass_upper": "20", "msfragger.precursor_true_tolerance": "20", "msfragger.precursor_true_units": "1", "msfragger.remainder_fragment_masses": "", "msfragger.remove_precursor_peak": "1", "msfragger.report_alternative_proteins": "true", "msfragger.restrict_deltamass_to": "all", "msfragger.run-msfragger": "true", "msfragger.search_enzyme_cut_1": "KR", "msfragger.search_enzyme_cut_2": "", "msfragger.search_enzyme_name_1": "stricttrypsin", "msfragger.search_enzyme_name_2": "null", "msfragger.search_enzyme_nocut_1": "", "msfragger.search_enzyme_nocut_2": "", "msfragger.search_enzyme_sense_1": "C", "msfragger.search_enzyme_sense_2": "C", "msfragger.table.fix-mods": "0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1", "msfragger.table.var-mods": "15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1", "msfragger.track_zero_topN": "0", "msfragger.use_all_mods_in_first_search": "false", "msfragger.use_topN_peaks": "150", "msfragger.write_calibrated_mzml": "false", "msfragger.write_uncalibrated_mgf": "false", "msfragger.zero_bin_accept_expect": "0", "msfragger.zero_bin_mult_expect": "1", "opair.activation1": "HCD", "opair.activation2": "HCD", "opair.glyco_db": "", "opair.max_glycans": "2", "opair.max_isotope_error": "2", "opair.min_isotope_error": "0", "opair.ms1_tol": "20", "opair.ms2_tol": "20", "opair.reverse_scan_order": "false", "opair.run-opair": "false", "opair.single_scan_type": "false", "peptide-prophet.cmd-opts": "--decoyprobs --ppm --accmass --nonparam --expectscore", "peptide-prophet.combine-pepxml": "false", "peptide-prophet.run-peptide-prophet": "false", "percolator.cmd-opts": "--only-psms --no-terminate --post-processing-tdc", "percolator.keep-tsv-files": "false", "percolator.min-prob": "0.5", "percolator.run-percolator": "true", "phi-report.dont-use-prot-proph-file": "false", "phi-report.filter": "--sequential --prot 0.01", "phi-report.pep-level-summary": "false", "phi-report.philosoher-msstats": "false", "phi-report.print-decoys": "false", "phi-report.prot-level-summary": "true", "phi-report.remove-contaminants": "false", "phi-report.run-report": "true", "protein-prophet.cmd-opts": "--maxppmdiff 2000000", "protein-prophet.run-protein-prophet": "true", "ptmprophet.cmdline": "KEEPOLD STATIC EMptmprophet.run-ptmprophet\\", "ptmprophet.run-ptmprophet": "false", "ptmshepherd.adv_params": "false", "ptmshepherd.annotation-common": "false", "ptmshepherd.annotation-custom": "false", "ptmshepherd.annotation-glyco": "false", "ptmshepherd.annotation-unimod": "true", "ptmshepherd.annotation_file": "", "ptmshepherd.annotation_tol": "0.01", "ptmshepherd.cap_y_ions": "", "ptmshepherd.decoy_type": "1", "ptmshepherd.diag_ions": "", "ptmshepherd.diagextract_mode": "false", "ptmshepherd.diagmine_diagMinFoldChange": "3.0", "ptmshepherd.diagmine_diagMinSpecDiff": "25", "ptmshepherd.diagmine_fragMinFoldChange": "3.0", "ptmshepherd.diagmine_fragMinPropensity": "12.5", "ptmshepherd.diagmine_fragMinSpecDiff": "15", "ptmshepherd.diagmine_minIonsPerSpec": "2", "ptmshepherd.diagmine_minPeps": "25", "ptmshepherd.diagmine_mode": "false", "ptmshepherd.diagmine_pepMinFoldChange": "3.0", "ptmshepherd.diagmine_pepMinSpecDiff": "25", "ptmshepherd.glyco_adducts": "", "ptmshepherd.glyco_fdr": "0.01", "ptmshepherd.glyco_isotope_max": "3", "ptmshepherd.glyco_isotope_min": "-1", "ptmshepherd.glyco_mode": "true", "ptmshepherd.glyco_ppm_tol": "50", "ptmshepherd.glycodatabase": "", "ptmshepherd.histo_smoothbins": "2", "ptmshepherd.iontype_a": "false", "ptmshepherd.iontype_b": "true", "ptmshepherd.iontype_c": "false", "ptmshepherd.iontype_x": "false", "ptmshepherd.iontype_y": "true", 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"ptmshepherd.spectra_ppmtol": "20", "ptmshepherd.varmod_masses": "", "quantitation.run-label-free-quant": "true", "run-psm-validation": "true", "run-validation-tab": "true", "saintexpress.fragpipe.cmd-opts": "", "saintexpress.max-replicates": "10", "saintexpress.run-saint-express": "false", "saintexpress.virtual-controls": "100", "speclibgen.easypqp.extras.max_delta_ppm": "15", "speclibgen.easypqp.extras.max_delta_unimod": "0.02", "speclibgen.easypqp.extras.rt_lowess_fraction": "0.01", "speclibgen.easypqp.fragment.a": "false", "speclibgen.easypqp.fragment.b": "true", "speclibgen.easypqp.fragment.c": "false", "speclibgen.easypqp.fragment.x": "false", "speclibgen.easypqp.fragment.y": "true", "speclibgen.easypqp.fragment.z": "false", "speclibgen.easypqp.im-cal": "Automatic selection of a run as reference IM", "speclibgen.easypqp.neutral_loss": "false", "speclibgen.easypqp.rt-cal": "noiRT", "speclibgen.easypqp.select-file.text": "", "speclibgen.easypqp.select-im-file.text": "", "speclibgen.keep-intermediate-files": "false", "speclibgen.run-speclibgen": "false", "tab-run.delete_calibrated_mzml": "false", "tab-run.delete_temp_files": "false", "tmtintegrator.add_Ref": "-1", "tmtintegrator.aggregation_method": "0", "tmtintegrator.allow_overlabel": "true", "tmtintegrator.allow_unlabeled": "true", "tmtintegrator.best_psm": "true", "tmtintegrator.channel_num": "TMT-6", "tmtintegrator.dont-run-fq-lq": "false", "tmtintegrator.glyco_qval": "-1", "tmtintegrator.groupby": "0", "tmtintegrator.log2transformed": "true", "tmtintegrator.max_pep_prob_thres": "0", "tmtintegrator.min_ntt": "0", "tmtintegrator.min_pep_prob": "0.9", "tmtintegrator.min_percent": "0.05", "tmtintegrator.min_purity": "0.5", "tmtintegrator.min_site_prob": "-1", "tmtintegrator.mod_tag": "none", "tmtintegrator.ms1_int": "true", "tmtintegrator.outlier_removal": "true", "tmtintegrator.print_RefInt": "false", "tmtintegrator.prot_exclude": "none", "tmtintegrator.prot_norm": "0", "tmtintegrator.psm_norm": 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