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02-download_​and_​analyze_​raw_​file

Adjust the settings herePath to the server and the actual installation,the mascot instrument and the toelerancesmust be adjusted in teh variable editor.The database, enzyme and modifications (andadditional parameters) must be set in theMascotAdapterOnline in the component.The decoy prefixes/regexes must be set in teh PIAnodes (in "process all IDs") and in the PeptideIndexerin "collect feature data". Node 136Node 401Node 403Node 405Node 593remove chromatogrampeak pick (if necessary / LTQ)remove ms1 for mascotNode 642create the tmpdir and prepare filevariablestemp analysis pathmascot labbeled resultsfinal adjustments formascot settings(tolerances, modifications)Node 866get runIdNode 890Node 891Column Resorter mascotidentifications all ID processing get creation date convert RAW to mzML ContainerInput (Table) ContainerOutput (Table) URL to FilePath (Variable) collectfeature data Column Appender filter raw spectra get ID-lessfile data Table Rowto Variable Create Temp Folder create temp filevalues (base names) Path to String(Variable) Java Edit Variable Container Input(Variable) RowID String to Path Column Filter Adjust the settings herePath to the server and the actual installation,the mascot instrument and the toelerancesmust be adjusted in teh variable editor.The database, enzyme and modifications (andadditional parameters) must be set in theMascotAdapterOnline in the component.The decoy prefixes/regexes must be set in teh PIAnodes (in "process all IDs") and in the PeptideIndexerin "collect feature data". Node 136Node 401Node 403Node 405Node 593remove chromatogrampeak pick (if necessary / LTQ)remove ms1 for mascotNode 642create the tmpdir and prepare filevariablestemp analysis pathmascot labbeled resultsfinal adjustments formascot settings(tolerances, modifications)Node 866get runIdNode 890Node 891 Column Resorter mascotidentifications all ID processing get creation date convert RAW to mzML ContainerInput (Table) ContainerOutput (Table) URL to FilePath (Variable) collectfeature data Column Appender filter raw spectra get ID-lessfile data Table Rowto Variable Create Temp Folder create temp filevalues (base names) Path to String(Variable) Java Edit Variable Container Input(Variable) RowID String to Path Column Filter

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: julian
Created at: 2019-11-14
On NodePit since: 2022-05-06
Last update: 2024-04-25
Created with KNIME version: v4.5.2

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