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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.

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 phosphorylation siteson 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 phosphorylation siteson 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

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