0 NextStep D:\Service\MHL\20200930\S\20200930_S_all.pdResult 1001 Undefined 068c1e4a-7e6d-427b-a151-3cba9120d58b Consensus CWF_Comprehensive_Enhanced Annotation_LFQ_and_Precursor_Quan 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 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/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 http://thermo.magellan.com/owl/DataTypes/Filtered True 10 10 ppm Coarse 0 0 ppm 0 5 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 Summed Abundances 3 Intensity True 0 Unique + Razor True True False Total Peptide Amount On All Average Use All Peptides Use All Peptides Exclude Modified Pairwise Ratio Based 100 None t-test (Background Based) 2 4 6 8 10 Only unique peptides based on protein groups False 1 InitialStep D:\Service\MHL\20200930\S\20200930_S_all.msf 1000 Running 5084c14d-2ad3-4008-bb0e-51e38c5146eb Processing PWF_Tribrid_MS2_LFQ_OT_HCD_SequestHT_Mascot_Percolator_Homosapiens_20200513 Processing workflow for precursor-based quantification. Ion trap-detected HCD spectra using SequestHT with Percolator validation. Specify the FASTA database, labels used, and any additional modifications. PD swissprot_human_202002.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 FTMS MS2 HCD + 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; swissprot_human_202002.fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 7 144 10 10 ppm 0.05 Da False False True True True True 0 1 0 0 1 0 4 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="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 http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/ScoredWithEValue http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys Default 0.05 Da True True True False False True False False False False False True False 0.01 0.05 30 20 ECD78FF9-3CF5-4AF6-A7D1-250925C55BA7 E6E22773-E9A6-4a26-9694-1CA77A797099 1024 90 20 http://desktop-ulmp0ti/mascot/ 0 Contaminants_20200624; swissprot_human_202002 Trypsin <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 All entries False 10 ppm False False Oxidation (M) Acetyl (Protein N-term) Carbamidomethyl (C) True False http://thermo.magellan.com/owl/DataTypes/Validated 5 0.2 3 High 0 True 2 Peaks (z <=2 ) / 3 Peaks (z >= 3) <unknown> Untargeted