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Proteomics_​LFQ

Combines peptide identifications from X!Tandem and Comet.
Uses normalized feature intensities for peptide quantification.
No smart protein inference, all possible proteins are reported for each peptide.

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.

Basic data analysis. Peptide quantities Proteomics Identification and Quantification using a Consensus ID approach between two search toolsCombines peptide identifications from X!Tandem and Comet.Uses normalized feature intensities for peptide quantification.No smart protein inference, all possible proteins are reported for each peptide. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizePlot intensity distributionLogarithmizeSelect intensitiesPlot intensity distributionFeaturedetectionMap IDson featuresNormalizeintensitiesRTalignmentLink correspondingfeaturesacross runsIdentificationsConsensus identificationsIdentificationsmapped to featuresSpectra (*.mzML)Database (*.fasta) ZipLoopStart ZipLoopEnd Row Splitter Column Filter R Snippet Box Plot (local) R Snippet Column Filter Box Plot (local) FeatureFinderCentroided IDMapper ConsensusMapNormalizer MapAlignerPoseClustering FeatureLinkerUnlabeledQT ID and Consensus ID MzTabExporter MzTabReader Histogram (local) MzTabReader MzTabExporter Histogram (local) IDConflictResolver File Exporter File Exporter File Exporter File Exporter File Importer File Importer Basic data analysis. Peptide quantities Proteomics Identification and Quantification using a Consensus ID approach between two search toolsCombines peptide identifications from X!Tandem and Comet.Uses normalized feature intensities for peptide quantification.No smart protein inference, all possible proteins are reported for each peptide. Seperate human spike-inpeptides from backgroundSelect intensitiesLogarithmizePlot intensity distributionLogarithmizeSelect intensitiesPlot intensity distributionFeaturedetectionMap IDson featuresNormalizeintensitiesRTalignmentLink correspondingfeaturesacross runsIdentificationsConsensus identificationsIdentificationsmapped to featuresSpectra (*.mzML)Database (*.fasta) ZipLoopStart ZipLoopEnd Row Splitter Column Filter R Snippet Box Plot (local) R Snippet Column Filter Box Plot (local) FeatureFinderCentroided IDMapper ConsensusMapNormalizer MapAlignerPoseClustering FeatureLinkerUnlabeledQT ID and Consensus ID MzTabExporter MzTabReader Histogram (local) MzTabReader MzTabExporter Histogram (local) IDConflictResolver File Exporter File Exporter File Exporter File Exporter 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
Created by: walzer
Created at: 2014-08-25
On NodePit since: 2023-05-06
Last update: 2024-11-17
Created with KNIME version: v4.7.2
Tags: OpenMSMass spectrometryPeptide identificationProtein identificationProtein quantification

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