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MS3 Search Settings" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Use MS(n - 1) with Parent Precursors">Use MS(n - 1) with Parent Precursors</ProcessingNodeParameter> <ProcessingNodeParameter Name="Ms2ToleranceForMS3" FriendlyName="MS3 tolerance" Category="2. MS3 Search Settings" IsAdvanced="False" IntendedPurpose="FragmentMassTolerance" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="20 ppm">20 ppm</ProcessingNodeParameter> <ProcessingNodeParameter Name="AlwaysCreateMS2Spectra" FriendlyName="Create MS2 Spectra" Category="2. MS3 Search Settings" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter> <ProcessingNodeParameter Name="ScoreBoostSameHit" FriendlyName="Boost" Category="2. MS3 Search Settings" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="20">20</ProcessingNodeParameter> <ProcessingNodeParameter Name="IsotopicPeakMzTolerance" FriendlyName="Isotopic Peak Tolerance" Category="2. MS3 Search Settings" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0.01">0.01</ProcessingNodeParameter> <ProcessingNodeParameter Name="MaximumIntensityDifference" FriendlyName="Maximum Intensity Difference" Category="2. MS3 Search Settings" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0.3">0.3</ProcessingNodeParameter> <ProcessingNodeParameter Name="MaximumConsideredPrecursorCharge" FriendlyName="Maximum Considered Precursor Charge" Category="2. MS3 Search Settings" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="4">4</ProcessingNodeParameter> <ProcessingNodeParameter Name="DecoyGenerationStrategyString" FriendlyName="Decoy generation strategy" Category="4. Decoy Settings" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="Reverse Protein Sequences">Reverse Protein Sequences</ProcessingNodeParameter> <ProcessingNodeParameter Name="RecalculateDecoys" FriendlyName="Recalculate decoys" Category="4. Decoy Settings" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter> <ProcessingNodeParameter Name="StatMod1" FriendlyName="1. Static Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Carbamidomethyl / +57.021 Da (C)"><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" /></ProcessingNodeParameter> <ProcessingNodeParameter Name="StatMod2" FriendlyName="2. Static Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="StatMod3" FriendlyName="3. Static Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="StatNMod" FriendlyName="Static Peptide N-Terminal Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="StatCMod" FriendlyName="Static Peptide C-Terminal Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="StatNModProtein" FriendlyName="Static Protein N-Terminal Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="SemiStatNMod" FriendlyName="Semi-Static Peptide N-Terminal Modification" Category="4. Static Modifications" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod1" FriendlyName="1. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Oxidation / +15.995 Da (M)"><Modification Version="2" AminoAcids="M" Name="Oxidation" Abbreviation="Oxidation" ID="46" UnimodAccession="35" DeltaMass="15.99492" DeltaAverageMass="15.99940" IsSubstitution="False" LeavingGroup="" Substitution="O" PositionType="Any" /></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod2" FriendlyName="2. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod3" FriendlyName="3. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod4" FriendlyName="4. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod5" FriendlyName="5. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod6" FriendlyName="6. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod7" FriendlyName="7. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod8" FriendlyName="8. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod9" FriendlyName="9. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod10" FriendlyName="10. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod11" FriendlyName="11. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod12" FriendlyName="12. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod13" FriendlyName="13. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod14" FriendlyName="14. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod15" FriendlyName="15. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod16" FriendlyName="16. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod17" FriendlyName="17. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod18" FriendlyName="18. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod19" FriendlyName="19. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynMod20" FriendlyName="20. Dynamic Modification" Category="5. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter> <ProcessingNodeParameter Name="DynNMod" FriendlyName="21. Dynamic Peptide N-Terminal Modification" Category="5. 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