parameter	value
process.emrt.minIntensity	750
process.emrt.minMass	500
process.emrt.rt.alignment.match.maxDeltaMass.ppm	10
process.emrt.rt.alignment.match.maxDeltaDriftTime	2
process.emrt.rt.alignment.normalizeReferenceTime	true
process.emrt.rt.alignment.maxProcesses	4
process.emrt.rt.alignment.referenceRun.selectionMethod	AUTO
process.emrt.clustering.preclustering.orderSequence	MTMTMT
process.emrt.clustering.preclustering.maxDistance.mass.ppm	6.06E-6
process.emrt.clustering.preclustering.maxDistance.time.min	0.202
process.emrt.clustering.preclustering.maxDistance.drift	2.02
process.emrt.clustering.distance.unit.mass.ppm	6.0E-6
process.emrt.clustering.distance.unit.time.min	0.2
process.emrt.clustering.distance.unit.drift.bin	2
process.emrt.clustering.dbscan.minNeighborCount	2
process.normalization.lowess.bandwidth	0.3
process.normalization.orderSequence	XPIR
process.normalization.minIntensity	3000
process.identification.peptide.minReplicationRate	1
process.identification.peptide.minScore	0
process.identification.peptide.minOverallMaxScore	0
process.identification.peptide.minSequenceLength	6
process.identification.peptide.acceptType.PEP_FRAG_1	true
process.identification.peptide.acceptType.IN_SOURCE	false
process.identification.peptide.acceptType.MISSING_CLEAVAGE	true
process.identification.peptide.acceptType.NEUTRAL_LOSS_H20	false
process.identification.peptide.acceptType.NEUTRAL_LOSS_NH3	false
process.identification.peptide.acceptType.PEP_FRAG_2	true
process.identification.peptide.acceptType.DDA	true
process.identification.peptide.acceptType.VAR_MOD	true
process.identification.peptide.acceptType.PTM	true
process.annotation.peptide.maxSequencesPerEMRTCluster	1
process.annotation.protein.resolveHomology	true
process.annotation.peptide.maxFDR	0.01
process.annotation.useSharedPeptides	razor
process.quantification.peptide.minMaxScorePerCluster	5
process.quantification.peptide.acceptType.IN_SOURCE	false
process.quantification.peptide.acceptType.MISSING_CLEAVAGE	true
process.quantification.peptide.acceptType.NEUTRAL_LOSS_H20	false
process.quantification.peptide.acceptType.NEUTRAL_LOSS_NH3	false
process.quantification.peptide.acceptType.PEP_FRAG_1	true
process.quantification.peptide.acceptType.PEP_FRAG_2	false
process.quantification.peptide.acceptType.VAR_MOD	true
process.quantification.peptide.acceptType.PTM	true
process.quantification.peptide.acceptType.DDA	true
process.quantification.topx.degree	3
process.quantification.topx.allowDifferentPeptides	true
process.quantification.minPeptidesPerProtein	2
process.quantification.absolute.standard.entry	CLPB_ECODH
process.quantification.absolute.standard.fmol	45
process.quantification.topx.allowDifferentPeptides	true
process.quantification.absolute.standard.entry	CLPB_ECODH
process.quantification.absolute.standard.fmol	45
process.quantification.maxProteinFDR	0.01