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QC_​with_​OpenMS

Uses X!Tandem to identify peptides and then uses various Meta Nodes for QC metrics.
Requires mzML spectrum files as input, and a protein database has to be specified in fasta format within the ID meta node.
The outputs are various tables and visualizations found in the QC meta nodes.

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/

Example workflow using the QC Meta NodesUses X!Tandem to identify peptides and then uses various MetaNodes for QC metrics.Requires mzML spectrum files as input, and a protein databasehas to be specified in fasta format within the ID meta node.The outputs are various tables and visualizations found in theQC meta nodes. Additional input:theoretical precursor masses to compare to peptideidentification results. Node 2Node 4set protein databasein herecreates TICplotcreates featurespace plotcreates plot of measuredvs.identifiedcreates mass accuracy plotsNode 137Node 138Node 139Node 140spectra input files (.mzML)protein database (.fasta)Node 144Node 145ZipLoopStart ZipLoopEnd ID TIC PeptidogenicFeaturespace Plot ID Ratio Mass accuracy FeatureFinderCentroided IDMapper QCCalculator QCShrinker File Importer File Importer File Exporter Explorer Browser Example workflow using the QC Meta NodesUses X!Tandem to identify peptides and then uses various MetaNodes for QC metrics.Requires mzML spectrum files as input, and a protein databasehas to be specified in fasta format within the ID meta node.The outputs are various tables and visualizations found in theQC meta nodes. Additional input:theoretical precursor masses to compare to peptideidentification results. Node 2Node 4set protein databasein herecreates TICplotcreates featurespace plotcreates plot of measuredvs.identifiedcreates mass accuracy plotsNode 137Node 138Node 139Node 140spectra input files (.mzML)protein database (.fasta)Node 144Node 145ZipLoopStart ZipLoopEnd ID TIC PeptidogenicFeaturespace Plot ID Ratio Mass accuracy FeatureFinderCentroided IDMapper QCCalculator QCShrinker File Importer File Importer File Exporter Explorer Browser

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
On NodePit since: 2018-06-16
Last update: 2024-12-18
Created with KNIME version: v5.2.1
Tags: OpenMSMass spectrometryQC

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