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ProteomicsLFQ_​tool_​and_​MSstats_​postprocessing

Uses the ProteomicsLFQ that contains the standard proteomics LFQ pipeline, after peptide and protein identification.
Applies post-processing with MSstats.

Example input data:
To download the data from the archive, check the box on the folder and click on the download button (arrow) on the top left.
Download and unpack the "iPRG2015" data into a directory "Example_data/iPRG2015" next to this workflow 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/Data/

To create a target+decoy databaseuse this node with your protein database in fasta format + (optionally butrecommended) a contaminant database like CRAP Note: reset first before changing theexperimental design. startKNIME workspaceand load data into MSstatsformatQC plotsall resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-Fwrite allplots to a folderinteractive editorGroup comparisons(and rename spike-ins with fake IDs)Node 49mzTab table formatmzml filesfastaNode 101Node 102Node 103Node 104Table to R R View (Workspace) R to Table R to Table R View (Workspace) R to Table Experimental Design DecoyDatabase PeptideIdentification R to R ProteomicsLFQ MzTabReader File Importer File Importer URI Port toVariable CSV Reader String to Path(Variable) File Exporter To create a target+decoy databaseuse this node with your protein database in fasta format + (optionally butrecommended) a contaminant database like CRAP Note: reset first before changing theexperimental design. startKNIME workspaceand load data into MSstatsformatQC plotsall resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-Fwrite allplots to a folderinteractive editorGroup comparisons(and rename spike-ins with fake IDs)Node 49mzTab table formatmzml filesfastaNode 101Node 102Node 103Node 104Table to R R View (Workspace) R to Table R to Table R View (Workspace) R to Table Experimental Design DecoyDatabase PeptideIdentification R to R ProteomicsLFQ MzTabReader File Importer File Importer URI Port toVariable CSV Reader String to Path(Variable) File Exporter

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: sachs
Created at: 2019-11-11
On NodePit since: 2022-03-01
Last update: 2025-05-01
Created with KNIME version: v5.4.0
Tags: OpenMSMass spectrometryProtein identificationProtein quantificationMSstats

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