0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_1.pdResult 142 Waiting 1985cefe-a8c7-4de2-9c90-5d05c555686a Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_1.msf 141 Undefined 7884ebab-9017-4ba8-8885-9466800247d6 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_2.pdResult 144 Waiting 212cc611-6f8b-4c67-a6f2-046a6dc96163 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_2.msf 143 Waiting 5cba2755-6ad6-4dd9-8b3b-a4a31cc37cb0 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_3.pdResult 146 Waiting 59ee85e0-2991-4d29-9f01-72f5dbc0b5ef Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S1_3.msf 145 Waiting afe647c3-4e48-495b-85da-1d758372255f Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_1.pdResult 148 Waiting b99cf9b1-68ab-4ffd-850b-fa1fdb627683 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_1.msf 147 Waiting 5aea775a-4906-41b3-864b-f69e67f1310b Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_2.pdResult 150 Waiting f078246e-545e-45f4-8751-c4fff0e75ddf Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_2.msf 149 Waiting 8b3f9bbf-2eaf-4147-8a31-df433af9f1c2 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_3.pdResult 152 Waiting 4a054cde-e53a-45aa-b7fe-f1732efb199c Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S2_3.msf 151 Waiting 5fa2a194-35cd-4dc1-b4d1-3fa42ec35908 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_1.pdResult 154 Waiting a3596b0b-858e-4ca4-a332-cd3bb0c1b91f Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_1.msf 153 Waiting 35956c59-8e09-4159-9244-c0d0bb2ab50e Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_2.pdResult 156 Waiting e0fa7a4e-0789-450c-b5fa-64a8c482c781 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_2.msf 155 Waiting 5f0eb2d1-a2b5-4cb6-8116-13665f4bb517 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_3.pdResult 158 Waiting 02613f83-f981-4d4d-a39e-93344304de13 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S3_3.msf 157 Waiting 8434b60f-fb1a-4ca0-b40a-619519f56d6c Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_1.pdResult 160 Waiting 1aa2acee-b3a8-41ea-ad77-1a7346d3c116 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_1.msf 159 Waiting 88d1eb2e-bfd7-4468-94f7-a27d9fa92595 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_2.pdResult 162 Waiting 816df0a0-2639-4d04-a6b2-9771b089fa47 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_2.msf 161 Waiting 94ee0f0a-3caf-482f-928d-74578dc7d8c5 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_3.pdResult 164 Waiting 8d4739ef-515b-471b-ba9d-e857085b5959 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S4_3.msf 163 Waiting da83e455-f86f-4cfb-88ab-776318dacaee Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_1.pdResult 166 Waiting 6e8c853e-8002-4e05-aa77-12391b0445cf Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_1.msf 165 Waiting 455af95e-224c-4155-9be9-8b852cf70d00 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_2.pdResult 168 Waiting 7e81ae2b-d0a0-4776-97fb-3ead5e8f61aa Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_2.msf 167 Waiting 98aa75f0-3c80-47f8-985e-4f777ed48738 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_3.pdResult 170 Waiting a03250a1-98ad-4c9d-be82-2b28e42ad0e2 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S5_3.msf 169 Waiting 53e0c563-f05a-40bd-87ec-1353f08fc625 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_1.pdResult 172 Waiting 6aebad65-bbc4-4224-9636-f138843b67be Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_1.msf 171 Waiting c8dd4061-7664-4f71-81f4-3a59c68052d5 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_2.pdResult 174 Waiting 36ccf671-fb32-4229-a21e-b1f590a4d6e0 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_2.msf 173 Waiting beea988b-e3ec-458b-8b45-79da23b8f13b Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05 0 NextStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_3.pdResult 176 Waiting d88e4a37-1fb0-4dff-b660-23043e7f3d25 Consensus CWF_Comprehensive_Enhanced Annotation_08012021 Result filtered for high confident peptides, with enhanced peptide and protein annotations. Add FASTA file with common contaminants to the Protein Marker node. Quan abunaces are normalized to the same total peptide amount per channel and scaled, so that the average abunce per protein and peptide is 100. http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified All Globally by Search Engine Type 0.05 0 0 ppm 0 0 0 0 0 0 0 0 0 0 Mascot: Ions Score; Sequest HT: XCorr; SEQUEST: XCorr; MSPepSearch: dot Score; MSPepSearch: rev-dot Score; MSPepSearch: MSPepSearch Score; PMI-Byonic: |Log Prob|; PMI-Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/WithDecoys Automatic (Control peptide level error rate if possible) 0.01 0.05 0.01 0.05 q-Value Concatenated False http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered High False 6 False 1 False False http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore True http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation http://thermo.magellan.com/owl/DataTypes/AnnotatedWithPeptideInProteinInformation True 1 75 Only for Master Proteins All And Specific High True Only for Master Proteins http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 http://thermo.magellan.com/owl/DataTypes/Filtered http://webservice.proteincenter.thermofisher.com/ProXweb/ 3 90 15 Biological Process Cellular Component Molecular Function None None None uniprot-Mus+musculus (1).fasta http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Classified contaminants.fasta False False False False True True ### Master Proteins Default Filter:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'FilterConditionProperties/FilterScope' 'FilterConditionProperties/FilterScopeValueMainGrid' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' ### Filter Set MasterProteinFilter.filterset contains the following filters:; ### Row Filter for TargetProtein:; ### Master is equal to Master; ###; ; 'magellan filter set' 1 'MasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' Only unique peptides based on protein groups 1 InitialStep D:\Raw and analysed lcms data\AMIT\vipin\12012021\Individual\S6_3.msf 175 Waiting 77a15a92-6f86-4ffe-b229-19c092bb3ff7 Processing PWF_QE_Basic_SequestHT_Percolator_08012021 Processing workflow for precursor-based quantification, using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 20 ppm 0.5 Da CID: by; HCD: by; ECD: cyz; ETD: cyz; EThcD: bcyz; UVPD: abxyz <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> Non-linear Regression Coarse http://thermo.magellan.com/owl/DataTypes/CentroidData http://thermo.magellan.com/owl/DataTypes/ProfileData Use MS1 Precursor PD True True Automatic True Averagine True 0 0 0 0 0 0 350 Da 5000 Da 0 1 (Not specified) Is Not MS1 (Not specified) 0 1000 Is Full (Not specified) 1.5 Automatic ITMS MS2 CID + 60000 30000 2.5 Da 5.5 Da http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys contaminants.fasta; uniprot-Mus+musculus (1).fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 6 144 10 10 ppm 0.02 Da False False True True True True 0 1 0 0 1 0 3 4 <Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="45" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /> <Modification Version="2" AminoAcids="N-Terminus" Name="Acetyl" Abbreviation="Acetyl" ID="2" UnimodAccession="1" DeltaMass="42.01057" DeltaAverageMass="42.03670" IsSubstitution="False" LeavingGroup="" Substitution="H(2) C(2) O" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss" Abbreviation="Met-loss" ID="664" UnimodAccession="765" DeltaMass="-131.04049" DeltaAverageMass="-131.19610" IsSubstitution="False" LeavingGroup="" Substitution="H(-9) C(-5) N(-1) O(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="M" Name="Met-loss+Acetyl" Abbreviation="Met-loss+Acetyl" ID="665" UnimodAccession="766" DeltaMass="-89.02992" DeltaAverageMass="-89.15940" IsSubstitution="False" LeavingGroup="" Substitution="H(-7) C(-3) N(-1) S(-1)" PositionType="Protein_N_Terminus" /> <Modification Version="2" AminoAcids="C" Name="Carbamidomethyl" Abbreviation="Carbamidomethyl" ID="8" UnimodAccession="4" DeltaMass="57.02146" DeltaAverageMass="57.05130" IsSubstitution="False" LeavingGroup="" Substitution="H(3) C(2) N O" PositionType="Any" /> True 3000 0 1.5 0.7 2 0.9 2.5 1.2 3 1.5 1.2 0.7 1.9 0.8 2.3 1 2.6 1.2 False 2.3 1.5 2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903 39EFA907-9435-46E1-9AF8-1203D547387A True False http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithPEP http://thermo.magellan.com/owl/DataTypes/ScoredWithQValue http://thermo.magellan.com/owl/DataTypes/Validated Concatenated q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 True 0.05 0 0.01 0.05