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Metabolite_​ID

Quantification and identification via accurate mass search with downstream processing and visualisation.

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 "Example_Data" data into a directory "Example_data" right inside your KNIME workspace.

URL: Home of the OpenMS plugin https://www.openms.de/
URL: Example Data https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/

Statistical Analysis Log scaling + Mediannormalization Intensity distributionsbefore normalization Intensity distributions afternormalization Hypothesis testing (t-test),FC filtering FDRcalculation /filtering Resultsto Excel Signal processing LoadmzML Mass trace extraction Retention time correctionand linking Identification using accurate mass search Structuremapping files Data Preparation Quant Data Preparation ID Data Preparation for Reporting Advanced Visualization Interactive Visualization Metabolomics Accurate Mass IdentificationQuantification and identification via accurate masssearch with downstream processing and visualisation. fold change filtermedian normalizationt-testFDRCombine ID and Quantification DataConvert smile string to SMILElog scalingReannotate original intensitiesHeatmapAll featuresPCAHeatmapAll featureswith FC > 2log_2(FC)-log_10(p - value)abs(log(FC)) > 1p < 0.01p < 0.01InteractiveMake structuredrawableNode 239convert list of smiles to stringPositive AdductsNegativeAdductsHMDB Mapping FileHMDB 2 Struct MappingNode 268Node 269ZipLoopStart ZipLoopEnd Box Plot (legacy) Numeric RowSplitter R Snippet R Snippet R Snippet Joiner (deprecated) Molecule Type Cast Column Filter Column Filter Box Plot (legacy) R Snippet Column Filter Joiner (deprecated) Column Filter R View (Table) R View (Table) R View (Table) InteractiveTable (legacy) R Snippet Color Manager Size Manager Shape Manager Scatter Plot(legacy) Column to Grid RDKit From Molecule Read Quant. Data AccurateMassSearch FeatureFinderMetabo FileConverter MapAlignerPoseClustering FeatureLinkerUnlabeledQT Split CollectionColumn Column Rename(deprecated) MzTabReader String Manipulation File Importer File Importer File Importer File Importer File Importer Excel Writer Ungroup Statistical Analysis Log scaling + Mediannormalization Intensity distributionsbefore normalization Intensity distributions afternormalization Hypothesis testing (t-test),FC filtering FDRcalculation /filtering Resultsto Excel Signal processing LoadmzML Mass trace extraction Retention time correctionand linking Identification using accurate mass search Structuremapping files Data Preparation Quant Data Preparation ID Data Preparation for Reporting Advanced Visualization Interactive Visualization Metabolomics Accurate Mass IdentificationQuantification and identification via accurate masssearch with downstream processing and visualisation. fold change filtermedian normalizationt-testFDRCombine ID and Quantification DataConvert smile string to SMILElog scalingReannotate original intensitiesHeatmapAll featuresPCAHeatmapAll featureswith FC > 2log_2(FC)-log_10(p - value)abs(log(FC)) > 1p < 0.01p < 0.01InteractiveMake structuredrawableNode 239convert list of smiles to stringPositive AdductsNegativeAdductsHMDB Mapping FileHMDB 2 Struct MappingNode 268Node 269ZipLoopStart ZipLoopEnd Box Plot (legacy) Numeric RowSplitter R Snippet R Snippet R Snippet Joiner (deprecated) Molecule Type Cast Column Filter Column Filter Box Plot (legacy) R Snippet Column Filter Joiner (deprecated) Column Filter R View (Table) R View (Table) R View (Table) InteractiveTable (legacy) R Snippet Color Manager Size Manager Shape Manager Scatter Plot(legacy) Column to Grid RDKit From Molecule Read Quant. Data AccurateMassSearch FeatureFinderMetabo FileConverter MapAlignerPoseClustering FeatureLinkerUnlabeledQT Split CollectionColumn Column Rename(deprecated) MzTabReader String Manipulation File Importer File Importer File Importer File Importer File Importer Excel Writer Ungroup

Nodes

Extensions

Links

Download

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

Download Workflow
On NodePit since: 2018-06-16
Last update: 2024-12-18
Created with KNIME version: v5.2.1
Tags: OpenMSMass spectrometryMetabolomics

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