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01-PIA_​first_​analysis

This workflow is very basic. It performs a spectrumidentification using X!Tandem, followed by the proteininference with PIA. You can find tutorial input files athttps://hub.knime.com/julianu/spaces/PIA/latest/ orhttps://github.com/julianu/pia-tutorial Spectrum identification Skip identification run protein inferenceand filter PSMsThe inference per se isrelatively fast, but themapping to the mzMLfile may take some time.If you are not interested ininspecting spectra, you candelete the connection fromthe mzML Input node.Port to URIcompile spectrumidentifications forPIA analysisleave onlypsm_fdr_scoreungroup on scoresfor easier analysismzML Inputprotein databaseTo skip spectrum identification,point this node to the provided idXML fileand connect this node to the "Port to URI" aboveidentify MS spectraconnect peptidesto protein accessionsPIA Analysis Port to URI PIA Compiler Row Filter Ungroup Input File Input File Input File XTandemAdapter PeptideIndexer This workflow is very basic. It performs a spectrumidentification using X!Tandem, followed by the proteininference with PIA. You can find tutorial input files athttps://hub.knime.com/julianu/spaces/PIA/latest/ orhttps://github.com/julianu/pia-tutorial Spectrum identification Skip identification run protein inferenceand filter PSMsThe inference per se isrelatively fast, but themapping to the mzMLfile may take some time.If you are not interested ininspecting spectra, you candelete the connection fromthe mzML Input node.Port to URIcompile spectrumidentifications forPIA analysisleave onlypsm_fdr_scoreungroup on scoresfor easier analysismzML Inputprotein databaseTo skip spectrum identification,point this node to the provided idXML fileand connect this node to the "Port to URI" aboveidentify MS spectraconnect peptidesto protein accessionsPIA Analysis Port to URI PIA Compiler Row Filter Ungroup Input File Input File Input File XTandemAdapter PeptideIndexer

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
Created by: julian
Created at: 2017-11-29
On NodePit since: 2020-07-15
Last update: 2024-11-21
Created with KNIME version: v4.2.3

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