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labelfree_​with_​protein_​quantification

Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensities with ProteinQuantifier.
Input mzML spectra files are specified in the Input Files node.
The target protein database is specified in the Input File node within the ID meta node.
Outputs are multiple boxplots that can be opened by right click -> View Boxplot on the blue Boxplot nodes.

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/

Summarized protein quantities Single peptide quantities Label-free identification and quantificationIdentification with X!Tandem in the ID meta node, Protein Inferencewith Fido and protein quantification based on feature intensities withProteinQuantifier.Input mzML spectra files are specified in the Input Files node.The target protein database is specified in the Input File node withinthe ID meta node.Outputs are multiple boxplots that can be opened by right click ->View Boxplot on the blue Boxplot nodes. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizeLogarithmizeSelect intensitiesFiltering decoysSeperate human spike-inproteins from backgroundLogarithmizeSelect intensitiesLogarithmizeSelect intensitiesinput spectra (mzML)input database (FASTA)Plot intensity distributionPlot intensity distributionPlot intensity distributionPlot intensity distributionZipLoopStart ZipLoopEnd ID Row Splitter Column Filter R Snippet R Snippet Column Filter CSV Reader(deprecated) URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter R Snippet Column Filter R Snippet Column Filter FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer File Importer Box Plot Histogram Box Plot Box Plot Box Plot Summarized protein quantities Single peptide quantities Label-free identification and quantificationIdentification with X!Tandem in the ID meta node, Protein Inferencewith Fido and protein quantification based on feature intensities withProteinQuantifier.Input mzML spectra files are specified in the Input Files node.The target protein database is specified in the Input File node withinthe ID meta node.Outputs are multiple boxplots that can be opened by right click ->View Boxplot on the blue Boxplot nodes. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizeLogarithmizeSelect intensitiesFiltering decoysSeperate human spike-inproteins from backgroundLogarithmizeSelect intensitiesLogarithmizeSelect intensitiesinput spectra (mzML)input database (FASTA)Plot intensity distributionPlot intensity distributionPlot intensity distributionPlot intensity distributionZipLoopStart ZipLoopEnd ID Row Splitter Column Filter R Snippet R Snippet Column Filter CSV Reader(deprecated) URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter R Snippet Column Filter R Snippet Column Filter FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer File Importer Box Plot Histogram Box Plot Box Plot Box Plot

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 spectrometryPeptide identificationProtein identificationProtein quantification

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