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DIAMetAlyzer_​2.0

Uses Decoy generation from DDA data, targeted DIA analysis using OpenSWATH and pyprophet for statistical validation.

Example input data:
To download the data from the archive linked below, check the box on the folder and click on the download button (arrow) on the top left.
Download and unpack the "DIAMetAlyzer" data into a directory "Example_data/DIAMetAlyzer" inside your KNIME workspace.

To run the workfow:It works best to have a condaenvironment added to KNIME (File ->Preferences -> KNIME -> Python)Please install the following pythonpackages:numpy, pandas, pyprophet, pyopenms1) Specify Input Files (.mzML)2) Specify SIRIUS 4.9.0 executable3) Specify library files (mapping, struct)for AccurateMassSearch4) Input SWATH files (.mzML)5) Specify Path to pyprophet installation(PATH to pyprophet)6) Specify ouput path in output folder7) Run the workflow Metabolomics assay library constructionUses Decoy generation from DDA data, targeted DIAanalysis using OpenSWATH and pyprophet for statisticalvalidation. Connect this node to AssayGeneratorMetaboand set the input file to a SIRIUS executable,if it is not automatically found in your PATH Assay library generationPATH to pyprophetNode 372assy library informationDDA (.mzML)Reference libray (.pqp)AMS: MappingFilesAMS: StructFilesAMS: positive_adductsAMS: negative_adductsSIRIUS 4.9.0 executableChromatograms (.mzML)Quantification (.osw)DIA/SWATH (.mzML) AssayGeneratorMetabo OpenSwathWorkflow Merge Variables(deprecated) ZipLoopStart ZipLoopEnd Statisticalvalidation String Input(legacy) ZipLoopStart ZipLoopEnd feature detection, adductgrouping & accurate mass search FileFilter URI Port toVariable File Importer File Exporter File Importer File Importer File Importer File Importer File Importer File Exporter File Exporter File Importer To run the workfow:It works best to have a condaenvironment added to KNIME (File ->Preferences -> KNIME -> Python)Please install the following pythonpackages:numpy, pandas, pyprophet, pyopenms1) Specify Input Files (.mzML)2) Specify SIRIUS 4.9.0 executable3) Specify library files (mapping, struct)for AccurateMassSearch4) Input SWATH files (.mzML)5) Specify Path to pyprophet installation(PATH to pyprophet)6) Specify ouput path in output folder7) Run the workflow Metabolomics assay library constructionUses Decoy generation from DDA data, targeted DIAanalysis using OpenSWATH and pyprophet for statisticalvalidation. Connect this node to AssayGeneratorMetaboand set the input file to a SIRIUS executable,if it is not automatically found in your PATH Assay library generationPATH to pyprophetNode 372assy library informationDDA (.mzML)Reference libray (.pqp)AMS: MappingFilesAMS: StructFilesAMS: positive_adductsAMS: negative_adductsSIRIUS 4.9.0 executableChromatograms (.mzML)Quantification (.osw)DIA/SWATH (.mzML) AssayGeneratorMetabo OpenSwathWorkflow Merge Variables(deprecated) ZipLoopStart ZipLoopEnd Statisticalvalidation String Input(legacy) ZipLoopStart ZipLoopEnd feature detection, adductgrouping & accurate mass search FileFilter URI Port toVariable File Importer File Exporter File Importer File Importer File Importer File Importer File Importer File Exporter File Exporter File Importer

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: alka
Created at: 2018-03-18
On NodePit since: 2023-05-06
Last update: 2024-04-24
Created with KNIME version: v4.7.3
Tags: OpenMSMass spectrometryMetabolomicsOpenSWATHSWATHDIA

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