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Labelfree with Protein Quantification

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:
Download
Labelfree with Protein Quantification (Input Data)
available in the same KNIME Hub space as thos workflow.
Put the folder in your KNIME Workspace in the same directory as the workflow itself.

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 intensitiesSelect intensitiesFiltering decoysSeperate human spike-inproteins from backgroundSelect intensitiesSelect intensitiesMS Data (mzML)LogarithmizePlot intensity distributionLogarithmizePlot intensity distributionLogarithmizePlot intensity distributionLogarithmizePlot intensity distributionNode 204Node 205PEP distributionbefore FDR filteringDatabase (fasta) ZipLoopStart ZipLoopEnd ID Row Splitter Column Filter Column Filter URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter Column Filter Column Filter FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot CSV Reader String to Path(Variable) Histogram 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 intensitiesSelect intensitiesFiltering decoysSeperate human spike-inproteins from backgroundSelect intensitiesSelect intensitiesMS Data (mzML)LogarithmizePlot intensity distributionLogarithmizePlot intensity distributionLogarithmizePlot intensity distributionLogarithmizePlot intensity distributionNode 204Node 205PEP distributionbefore FDR filteringDatabase (fasta) ZipLoopStart ZipLoopEnd ID Row Splitter Column Filter Column Filter URI Port toVariable Row Filter Protein inferencewith FidoAdapter Row Splitter Column Filter Column Filter FeatureFinderCentroided FalseDiscoveryRate IDMapper IDMerger MapAlignerPoseClustering FeatureLinkerUnlabeledQT ConsensusMapNormalizer ProteinQuantifier MzTabExporter MzTabReader MzTabExporter MzTabReader IDConflictResolver File Importer Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot Math Formula(Multi Column) Box Plot CSV Reader String to Path(Variable) Histogram File Importer

Nodes

Extensions

Links

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

Download Workflow
On NodePit since: 2023-03-31
Last update: 2026-01-13
Created with KNIME version: v5.0.0
Tags: OpenMSMass spectrometryPeptide identificationProtein identificationProtein quantification

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