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02-PIA_​and_​quant

Workflow

combine identifications and map to features Align, link and normalize features spectrum identifications feature detection Basic Label Free Quantification WorkflowThe workflow first identifies the spectra using X!Tandem and detects the features with the FeatureFinderMultiplex.The spectrum identifications are also used for the protein inference before protein quantification.You can find tutorial input files athttps://hub.knime.com/julianu/spaces/PIA/latest/ orhttps://github.com/julianu/pia-tutorial protein inference for quantification quantify the proteins using the inference Protein SequenceDatabasecalculate FDR Scoretandem idinfere proteinsmzML filespeptidefeature detectionidentify MS spectrafilter forFDRScore <= 0.01combine featuresand spectrum IDsZipLoopStart ZipLoopEnd Input File ZipLoopStart ZipLoopEnd PIA Compiler PIA Analysis ZipLoopStart PIA Compiler PIA Analysis Port to URI ZipLoopEnd Port to URI URI Port toVariable CSV Reader do some minimalstatistics Input Files use original namesas PIA export names FeatureFinderCentroided XTandemAdapter IDFilter IDMapper MapAlignerIdentification FeatureLinkerUnlabeledQT ConsensusMapNormalizer IDConflictResolver ProteinQuantifier combine identifications and map to features Align, link and normalize features spectrum identifications feature detection Basic Label Free Quantification WorkflowThe workflow first identifies the spectra using X!Tandem and detects the features with the FeatureFinderMultiplex.The spectrum identifications are also used for the protein inference before protein quantification.You can find tutorial input files athttps://hub.knime.com/julianu/spaces/PIA/latest/ orhttps://github.com/julianu/pia-tutorial protein inference for quantification quantify the proteins using the inference Protein SequenceDatabasecalculate FDR Scoretandem idinfere proteinsmzML filespeptidefeature detectionidentify MS spectrafilter forFDRScore <= 0.01combine featuresand spectrum IDsZipLoopStart ZipLoopEnd Input File ZipLoopStart ZipLoopEnd PIA Compiler PIA Analysis ZipLoopStart PIA Compiler PIA Analysis Port to URI ZipLoopEnd Port to URI URI Port toVariable CSV Reader do some minimalstatistics Input Files use original namesas PIA export names FeatureFinderCentroided XTandemAdapter IDFilter IDMapper MapAlignerIdentification FeatureLinkerUnlabeledQT ConsensusMapNormalizer IDConflictResolver ProteinQuantifier

Download

Get this workflow from the following link: Download

Nodes

02-PIA_​and_​quant consists of the following 34 nodes(s):

Plugins

02-PIA_​and_​quant contains nodes provided by the following 6 plugin(s):