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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.

Summarized protein quantities Single peptide quantities Label-free identification and quantificationIdentification with X!Tandem in the ID meta node, Protein Inference with Fido and proteinquantification 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 theblue Boxplot nodes. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizePlot intensity distributionLogarithmizeSelect intensitiesPlot intensity distributionFiltering decoysSeperate human spike-inproteins from backgroundLogarithmizeSelect intensitiesLogarithmizeSelect intensitiesPlot intensity distributionPlot intensity distributionNode 183Node 186input spectra (mzML)input database (FASTA) ZipLoopStart ZipLoopEnd ID Row Splitter Column Filter R Snippet Box Plot (local) R Snippet Column Filter Box Plot (local) CSV Reader(deprecated) URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter R Snippet Column Filter R Snippet Column Filter Box Plot (local) Box Plot (local) FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter Histogram (local) MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer File Importer Summarized protein quantities Single peptide quantities Label-free identification and quantificationIdentification with X!Tandem in the ID meta node, Protein Inference with Fido and proteinquantification 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 theblue Boxplot nodes. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizePlot intensity distributionLogarithmizeSelect intensitiesPlot intensity distributionFiltering decoysSeperate human spike-inproteins from backgroundLogarithmizeSelect intensitiesLogarithmizeSelect intensitiesPlot intensity distributionPlot intensity distributionNode 183Node 186input spectra (mzML)input database (FASTA) ZipLoopStart ZipLoopEnd ID Row Splitter Column Filter R Snippet Box Plot (local) R Snippet Column Filter Box Plot (local) CSV Reader(deprecated) URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter R Snippet Column Filter R Snippet Column Filter Box Plot (local) Box Plot (local) FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter Histogram (local) MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer 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
On NodePit since: 2023-05-06
Last update: 2024-11-18
Created with KNIME version: v4.7.2
Tags: OpenMSMass spectrometryPeptide identificationProtein identificationProtein quantification

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