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 Best match standard 0.05 0 10 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 http://thermo.magellan.com/owl/DataTypes/Filtered True Coarse 10 10 ppm 0 0 ppm 0 5 15 ppm True 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/Validated http://thermo.magellan.com/owl/DataTypes/Quantified http://thermo.magellan.com/owl/DataTypes/Quantified http://thermo.magellan.com/owl/DataTypes/Quantified http://thermo.magellan.com/owl/DataTypes/Quantified http://thermo.magellan.com/owl/DataTypes/Quantified Unique + Razor True False False Intensity True 0 Total Peptide Amount On All Average Use All Peptides Use All Peptides Exclude Modified Summed Abundances 3 Pairwise Ratio Based 100 None t-test (Background Based) False 2 4 6 8 10 75 True None 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 Automatic 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/Classified False False False False True True True True True 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/Filtered http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 Only unique peptides based on protein groups ### This file contains the following filters:; ###; ### Row Filter for Proteins:; ### ------------------------------------; ### AND; ### |; ### +--Master is equal to Master; ### |; ### +--in category; ### |; ### +--Protein FDR Confidence; ### |; ### +--High; ### ------------------------------------; ###; ###; ### Row Filter for Input Files:; ### ------------------------------------; ### FileName does not end with msf; ### ------------------------------------; ###; ; 'magellan filter set' 1 'HighConfidentMasterProteinFilter.filterset' FiltersetProperties 1 'LastFileName' 'Z:\HighConfidentMasterProteinFilter.filterset' Filter 'AminoAcids' FilterProperties 1 'Filter/DisplayPropertyHint' 'Amino Acids' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' TRUE Filter 'DecoyPeptideGroup' FilterProperties 1 'Filter/DisplayPropertyHint' 'Decoy Peptide Groups' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'DecoyPeptideSpectrumMatch' FilterProperties 1 'Filter/DisplayPropertyHint' 'Decoy PSMs' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'DecoyProtein' FilterProperties 1 'Filter/DisplayPropertyHint' 'Decoy Proteins' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'DecoyProteinGroup' FilterProperties 1 'Filter/DisplayPropertyHint' 'Decoy Protein Groups' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'DecoyProteoformSpectrumMatch' FilterProperties 1 'Filter/DisplayPropertyHint' 'Decoy PrSMs' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'TargetProtein' FilterProperties 1 'Filter/DisplayPropertyHint' 'Proteins' 2 NARY_AND 2 = FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' datadistribution_particular FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinFDRConfidence' constant 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'position_id_1' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'TargetProteoformSpectrumMatch' FilterProperties 1 'Filter/DisplayPropertyHint' 'PrSMs' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' = property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'UnknownModification' FilterProperties 1 'Filter/DisplayPropertyHint' 'Unknown Modifications' 2 TRUE FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' TRUE Filter 'WorkflowInputFile' FilterProperties 1 'Filter/DisplayPropertyHint' 'Input Files' 2 NARY_AND 1 endsnotwith property 'System.String, mscorlib' 'FileName' constant 'System.String, mscorlib' 'msf' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' TRUE ###; ### This file contains the following filters:; ###; ### Row Filter for Proteins:; ### ------------------------------------; ### in category; ### |; ### +--Protein Group FDR Confidence; ### |; ### +--1; ### ------------------------------------; ###; ###; ### Row Filter for Protein Groups:; ### ------------------------------------; ### in category; ### |; ### +--Protein Group FDR Confidence; ### |; ### +--1; ### ------------------------------------; ###; ###; ### Row Filter for Input Files:; ### ------------------------------------; ### FileName does not end with msf; ### ------------------------------------; ###; 'magellan filter set' 2 'DisplayFilter.filterset' Filter 'TargetProtein' FilterProperties 1 'Filter/DisplayPropertyHint' 'Proteins' 2 NARY_AND 1 datadistribution_particular FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein Group FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinGroupFDRConfidence' constant 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'position_id_1' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' precise= property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'TargetProteinGroup' FilterProperties 1 'Filter/DisplayPropertyHint' 'Protein Groups' 1 NARY_AND 1 datadistribution_particular FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein Group FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinGroupFDRConfidence' constant 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'position_id_1' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' Filter 'WorkflowInputFile' FilterProperties 1 'Filter/DisplayPropertyHint' 'Input Files' 2 NARY_AND 1 endsnotwith property 'System.String, mscorlib' 'FileName' constant 'System.String, mscorlib' 'msf' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' TRUE <SummaryStatistics> <!-- * confident IDs (proteins, peptides, PSMs) by sample --> <Statistic> <ValueName>Protein Groups by Sample</ValueName> <Description> Number of detected protein groups by Sample </Description> <Operator>count</Operator> <Units>protein groups</Units> <Table>Proteins</Table> <Column min_value="0.0001">Abundances (Grouped)</Column> <Filter filename="HighConfident_ProteinGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped)"/> </GroupBy> </Statistic> <Statistic> <ValueName>Proteins by Sample</ValueName> <Description> Number of detected proteins by Sample </Description> <Operator>count</Operator> <Units>proteins</Units> <Table>Proteins</Table> <Column min_value="0.0001">Abundances (Grouped)</Column> <Filter filename="HighConfident_Proteins.filterset"/> <GroupBy> <Sample column="Abundances (Grouped)"/> </GroupBy> </Statistic> <Statistic> <ValueName>Peptides by Sample</ValueName> <Description> Number of detected peptides by Sample </Description> <Operator>count</Operator> <Units>peptides</Units> <Table>Peptide Groups</Table> <Column min_value="0.0001">Abundances (Grouped)</Column> <Filter filename="HighConfident_PeptideGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped)"/> </GroupBy> </Statistic> <Statistic> <ValueName>PSMs by File</ValueName> <Description> Number of confident PSMs by File </Description> <Operator>count</Operator> <Units>PSMs</Units> <Table>PSMs</Table> <Column>File ID</Column> <Filter filename="HighConfident_PSMs.filterset"/> <GroupBy> <File column="File ID"/> </GroupBy> </Statistic> <!-- * Median CVs of high confident (proteins, pcms) --> <Statistic> <ValueName>Protein Groups Median CV</ValueName> <Description> Median abundance CV of high confident protein groups by Sample </Description> <Operator>median</Operator> <Units>[%]</Units> <Table>Proteins</Table> <Column>Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_ProteinGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName>Proteins Median CV</ValueName> <Description> Median abundance CV of high confident proteins by Sample </Description> <Operator>median</Operator> <Units>[%]</Units> <Table>Proteins</Table> <Column>Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_Proteins.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName>Peptides Median CV</ValueName> <Description> Median abundance CV of high confident peptides by Sample </Description> <Operator>median</Operator> <Units>[%]</Units> <Table>Peptide Groups</Table> <Column>Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_PeptideGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <!-- * # high confident Protein groups, proteins, peptides under given % CV --> <Statistic> <ValueName># Protein Groups with CV under 10%</ValueName> <Description> The number of high confident protein groups having an abundance CV under 10% </Description> <Operator>count</Operator> <Units>protein groups</Units> <Table>Proteins</Table> <Column max_value="10">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_ProteinGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName># Protein Groups with CV under 20%</ValueName> <Description> The number of high confident protein groups having an abundance CV under 20% </Description> <Operator>count</Operator> <Units>protein groups</Units> <Table>Proteins</Table> <Column max_value="20">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_ProteinGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName># Proteins with CV under 10%</ValueName> <Description> The number of high confident proteins having an abundance CV under 10% </Description> <Operator>count</Operator> <Units>proteins</Units> <Table>Proteins</Table> <Column max_value="10">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_Proteins.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName># Proteins with CV under 20%</ValueName> <Description> The number of high confident proteins having an abundance CV under 20% </Description> <Operator>count</Operator> <Units>proteins</Units> <Table>Proteins</Table> <Column max_value="20">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_Proteins.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName># Peptides with CV under 10%</ValueName> <Description> The number of high confident peptides having an abundance CV under 10% </Description> <Operator>count</Operator> <Units>peptides</Units> <Table>Peptide Groups</Table> <Column max_value="10">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_PeptideGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <Statistic> <ValueName># Peptides with CV under 20%</ValueName> <Description> The number of high confident peptides having an abundance CV under 20% </Description> <Operator>count</Operator> <Units>peptides</Units> <Table>Peptide Groups</Table> <Column max_value="20">Abundances (Grouped) CVs [%]</Column> <Filter filename="HighConfident_PeptideGroups.filterset"/> <GroupBy> <Sample column="Abundances (Grouped) CVs [%]"/> </GroupBy> </Statistic> <!-- * Median ratios by (ratio) --> <Statistic> <ValueName>Median Protein Group Ratios</ValueName> <Description> Median protein group ratios by each calculated ratio </Description> <Operator>median</Operator> <Table>Proteins</Table> <Column>Abundance Ratios</Column> <Filter filename="HighConfident_ProteinGroups.filterset"/> <GroupBy> <Ratio column="Abundance Ratios"/> </GroupBy> </Statistic> <Statistic> <ValueName>Median Protein Ratios</ValueName> <Description> Median protein ratios by each calculated ratio </Description> <Operator>median</Operator> <Table>Proteins</Table> <Column>Abundance Ratios</Column> <Filter filename="HighConfident_Proteins.filterset"/> <GroupBy> <Ratio column="Abundance Ratios"/> </GroupBy> </Statistic> <Statistic> <ValueName>Median Peptide Ratios</ValueName> <Description> Median peptide ratios by each calculated ratio </Description> <Operator>median</Operator> <Table>Peptide Groups</Table> <Column>Abundance Ratios</Column> <Filter filename="HighConfident_PeptideGroups.filterset"/> <GroupBy> <Ratio column="Abundance Ratios"/> </GroupBy> </Statistic> </SummaryStatistics> ###; ### This file contains the following filters:; ###; ### Row Filter for Proteins:; ### ------------------------------------; ### Protein Group FDR Confidence in every category; ### ------------------------------------; ###; ###; ### Row Filter for Protein Groups:; ### ------------------------------------; ### Protein Group FDR Confidence in every category; ### ------------------------------------; ###; ; 'magellan filter set' 2 'HighConfident_ProteinGroups.filterset' FiltersetProperties 1 'LastFileName' 'D:\sumStats\HighConfident_ProteinGroups.filterset' Filter 'TargetProtein' FilterProperties 1 'Filter/DisplayPropertyHint' 'Proteins' 2 NARY_AND 1 datadistribution_every FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein Group FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinGroupFDRConfidence' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' precise= property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' Filter 'TargetProteinGroup' FilterProperties 1 'Filter/DisplayPropertyHint' 'Protein Groups' 1 NARY_AND 1 datadistribution_every FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein Group FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinGroupFDRConfidence' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' ###; ### This file contains the following filters:; ###; ### Row Filter for Proteins:; ### ------------------------------------; ### Protein FDR Confidence in every category; ### ------------------------------------; ###; ; 'magellan filter set' 2 'HighConfident_Proteins.filterset' FiltersetProperties 1 'LastFileName' 'D:\sumStats\HighConfident_Proteins.filterset' Filter 'TargetProtein' FilterProperties 1 'Filter/DisplayPropertyHint' 'Proteins' 2 NARY_AND 1 datadistribution_every FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Protein FDR Confidence' property 'Thermo.Magellan.EntityDataFramework.DataDistributionValue, Thermo.Magellan.EntityDataFramework' 'ProteinFDRConfidence' Filter '7899A5F8-6954-4E95-8C2D-BB0C83221B21' 1 datadistribution_level_equals property 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '6AED4774-1ECD-4202-B746-B79D936A3D77' constant 'System.Nullable`1[[System.Int32, mscorlib]], mscorlib' '4' FilterConditionProperties 1 'PredefinedProperty' 'ExcludedBy' precise= property 'System.Int32, mscorlib' 'ExcludedBy' constant 'System.Int32, mscorlib' '-1' ###; ### This file contains the following filters:; ###; ### Row Filter for Peptide Groups:; ### ------------------------------------; ### Confidence is equal to High; ### ------------------------------------; ###; ; 'magellan filter set' 2 'HighConfident_PeptideGroups.filterset' FiltersetProperties 1 'LastFileName' 'D:\sumStats\HighConfident_PeptideGroups.filterset' Filter 'TargetPeptideGroup' FilterProperties 1 'Filter/DisplayPropertyHint' 'Peptide Groups' 1 NARY_AND 1 precise= FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Confidence' property 'Thermo.Magellan.Proteomics.MatchConfidence, Thermo.Magellan.Proteomics' 'Confidence' constant 'Thermo.Magellan.Proteomics.MatchConfidence, Thermo.Magellan.Proteomics' 'High' ###; ### This file contains the following filters:; ###; ### Row Filter for PSMs:; ### ------------------------------------; ### Confidence is equal to High; ### ------------------------------------; ###; ; 'magellan filter set' 2 'HighConfident_PSMs.filterset' FiltersetProperties 1 'LastFileName' 'D:\sumStats\HighConfident_PSMs.filterset' Filter 'TargetPeptideSpectrumMatch' FilterProperties 1 'Filter/DisplayPropertyHint' 'PSMs' 1 NARY_AND 1 precise= FilterConditionProperties 1 'NamedComparableFilterCondition/DisplayPropertyHint' 'Confidence' property 'Thermo.Magellan.Proteomics.MatchConfidence, Thermo.Magellan.Proteomics' 'MatchConfidence' constant 'Thermo.Magellan.Proteomics.MatchConfidence, Thermo.Magellan.Proteomics' 'High'