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Phosphoproteomics_​ID

Uses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylation sites on peptide sequences and then Epifany for protein inference.

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/

Database search and annotation (target, decoy) Score estimation and site localization Score estimation and protein inference Identification of Phoshorylation sitesUses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylationsites on peptide sequences and then Epifany for protein inference. score calibrationPhospho sitelocalization5% PSM-FDRPEP as main scoreNode 241input (.mzML)output (.mzTab)target-decoy database (.fasta)Note: Build your own target-decoy database using the OpenMS DecoyDatabase tool.ZipLoopStart PercolatorAdapter ZipLoopEnd Protein inference Peptideidentification LuciphorAdapter IDFilter IDScoreSwitcher MzTabExporter File Importer File Exporter File Importer Database search and annotation (target, decoy) Score estimation and site localization Score estimation and protein inference Identification of Phoshorylation sitesUses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylationsites on peptide sequences and then Epifany for protein inference. score calibrationPhospho sitelocalization5% PSM-FDRPEP as main scoreNode 241input (.mzML)output (.mzTab)target-decoy database (.fasta)Note: Build your own target-decoy database using the OpenMS DecoyDatabase tool.ZipLoopStart PercolatorAdapter ZipLoopEnd Protein inference Peptideidentification LuciphorAdapter IDFilter IDScoreSwitcher MzTabExporter File Importer File Exporter 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: alka
Created at: 2019-04-29
On NodePit since: 2023-05-06
Last update: 2025-05-01
Created with KNIME version: v5.4.0
Tags: OpenMSMass spectrometryPeptide identificationProtein identification

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