0 NextStep 63 Undefined Consensus RamusFINAL http://thermo.magellan.com/owl/DataTypes/WithDecoys http://thermo.magellan.com/owl/DataTypes/WithDecoys Identified or Quantified Globally by Search Engine Type 10 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; Byonic: |Log Prob|; Byonic: Byonic Score; MS Amanda: Amanda Score Best match standard 75 Best Position 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 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 False 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/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Filtered http://thermo.magellan.com/owl/DataTypes/Validated 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 50000 mode(lowest) Medium 1 1 razor average sum 3 iBAQ False True True True <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 7 http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/Validated 0.01 0.05 1 InitialStep 62 Undefined 6e10eb81-0711-4329-bf4e-9595b35a3899 Processing RamusFINAL Use MS1 Precursor True 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 Saccharomyces cerevisiae S288c (SwissProt TaxID=559292).fasta; ups1-ups2-sequences.fasta <Enzyme Version="1" Name="Trypsin" CleavageSites="KR" CleavageInhibitors="P" Offset="1" CleavageSpecificity="SpecificAtBothEnds" /> 2 5 ppm 0.8 Da <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" /> <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" /> 3 4 1 2 6 b,y b,y; b,y,H2O,NH3; a,b,y,H2O,NH3; a,b,y,H2O,NH3,Imm; a,b,y; c,y,z+1,z+2; b,c,y,z+1,z+2 5 1 0 True True False False False False False 5 PD Determined PD Determined; Amanda Determined +2, +3 +2; +3; +2, +3; +2, +3, +4; +3, +4; +2, +3, +4, +5 False 100 0 0 120 90 False False False False False False False False False False B6D45BD3-F20E-4006-9156-C59899C35790 100% 200000 10000 100 True False 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 0.05 0 True 0.01 0.05 q-Value D0E5CE92-ABF5-43F1-8D0F-C17FC9194D99 http://thermo.magellan.com/owl/DataTypes/Validated http://thermo.magellan.com/owl/DataTypes/ScoredWithSiteLocalizationProbability <?xml version="1.0" encoding="UTF-8" standalone="yes"?>; <AnyPTM>; <!-- This defines a modifications. The unimodID can be found in (path can be slightly different; C:\ProgramData\Thermo\Proteome Discoverer 2.0\MagellanDBs\unimod.xml; -->; <modification name="Methyl" abbreviation="Methyl" searchdefined="FALSE" mass="14.015650" unimodId="34">; <!-- Targets of the modification -->; <target aminoacid="K"/>; <target aminoacid="R"/>; <!--; The modifications below this comment are substituted with the modification above this comment.; Hence, the name of the modifications below have to be identical to the name defined by the search engine.; Trivial substitution (Methyl = 1xMethyl) can also be performed (therefore all modifications will be scored together.; -->; <equivalentmodification name="Methyl" factor="1"/>; <equivalentmodification name="Dimethyl" factor="2"/>; <!--Since arginine does not carry 3 methyls avoid this target-->; <equivalentmodification name="Trimethyl" factor="3" avoidTarget="R"/>; <equivalentmodification name="Methyl (K)" factor="1"/>; <equivalentmodification name="Dimethyl (K)" factor="2"/>; </modification>; ; <!--EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE EXAMPLE-->; <modification name="ptmRS_BaseTestModification" abbreviation="baseTestMod" searchdefined="FALSE" mass="69.235469" unimodId="-9999">; <!-- Specifies a modification Test, which will, if on a peptide be used by ptmRS -->; <!-- Specify the targets for current modification. It is important to highlight that this targets are taken for scoring! -->; <target aminoacid="M"/>; <target aminoacid="P"/>; <target aminoacid="E"/>; ; <!--; Specify neutral losses. This NL will be used while scoring. Also NLs defined by the search engine will; be used. Each <target /> specifies an amino acid (and a number of modification) pair where this NL is possible; -->; <neutralloss abbreviation="NLofM" mass="98.12345">; <target aminoacid="M" factor ="3"/>; <target aminoacid="M" factor ="2"/>; <target aminoacid="M" factor ="1"/>; </neutralloss>; <neutralloss abbreviation="NLofPE" mass="59.3256">; <target aminoacid="P"/>; <target aminoacid="E"/>; </neutralloss>; ; <!--; Diagnostic ions (DI) can be defined. Currently 3 types of diagnostic ions are supported.; * First, ions giving evidence for a specific target (e.g. DI found, modification is on Lysine); * Second ions giving evidence for the number of modification on a target (e.g. DI found, modification is on any target with the a factor of 2, dimethyl on Lysine/Arginin).; * Third, combinations of both like in this example; * Last, just the report it.; -->; <diagnosticion name="Diagnostic Ion1" mass="55" peakdepth="8">; <!-- This diagnostic ions is an evidence that modification is bind to target M -->; <Evidence_Target>M</Evidence_Target>; <!-- This diagnostic ions is an evidence for this modification of a factor 3 -->; <Evidence_Factor>3</Evidence_Factor>; <!--; Defines the relativity of the given mass:; * Precursor: DI searched at: precursor + mass; * ExistingPrecursor (default): DI searched if the precursor was measured in MS2 at: precursor + mass; * ImoniumIon: The given mass is absolute, therefore here: mass; -->; <Relativity>ExistingPrecursor</Relativity>; </diagnosticion>; ; <!--; Following modifications are mapped onto the ptmRS_BaseTestModification:; Modification on PSMs with the name "ptmRS_SearchengineTestMod1" are mapped onto 1x ptmRS_BaseTestModification; -->; <equivalentmodification name="ptmRS_SearchengineTestMod1" factor="1" new="FALSE"/>; <!-- Modification on PSMs with the name "ptmRS_SearchengineTestMod2" are mapped onto 2x ptmRS_BaseTestModification (this 2x mod cannot be found on P,E)-->; <equivalentmodification name="ptmRS_SearchengineTestMod2" factor="2" new="FALSE" avoidTarget="PE"/>; <!-- Modification on PSMs with the name "ptmRS_SearchengineTestMod3" are mapped onto 3x ptmRS_BaseTestModification (this 3x mod cannot be found on P,E)-->; <equivalentmodification name="ptmRS_SearchengineTestMod3" factor="3" new="FALSE" avoidTarget="PE"/>; </modification>; ; <!-- Defines which fragment ions are used during the scoring in dependence of the activation type -->; <FragmentIonCompositionPreference>; <FragmentIonComposition ActivationType="CID" FragmentIonComposition="b,y" NeutralLossFragmentIonComposition=""/>; <FragmentIonComposition ActivationType="HCD" FragmentIonComposition="b,y" NeutralLossFragmentIonComposition="b,y"/>; <FragmentIonComposition ActivationType="ETHcD" FragmentIonComposition="b,y,c,zPrime,zRadical" NeutralLossFragmentIonComposition="b,y"/>; <FragmentIonComposition ActivationType="ETD" FragmentIonComposition="c,zPrime,zRadical" NeutralLossFragmentIonComposition=""/>; </FragmentIonCompositionPreference>; </AnyPTM> False True True 0.8 Da Automatic -2 8 False 500 10 5 0 0 http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore http://thermo.magellan.com/owl/DataTypes/WithDecoys High 7 70 1 5 ppm 0.5 2 True False False ptmRS [4]: Best Site Probabilities 75 2 10 True Rlm 1000 10 False 0.005 0.15 10000 True 0.3 percolator 0.01 0.05 True False DeltaM1; DeltaT1; DeltaT2; F1; F2; F3 5 True