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MSstats_​statPostProcessing_​iPRG2015

Uses MSstatsConverter to make tables that are processed in short R code scripts in various nodes.
A consensusXML file from an LFQ workflow is required as input.
The outputs are several images and tables accessible through richt clicking the R View and R to Table 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/

Connect and set output path in script towrite all plots to a folder Post-processing LFQ results with MSstatsUses MSstatsConverter to make tables that are processed in short R code scripts in various nodes.A consensusXML file from an LFQ workflow is required as input.The outputs are several images and tables accessible through richt clicking the R View and R to Tablenodes. Calculate groupcomparisonsof interestconsensusXMLto MSstats csvstartKNIME workspaceand load data into MSstatsformatQC plotsRename results(spike-ins havefake IDs)all resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-Fwrite allplots to a folderconsensusXMLwrite Filefor backupexperimental designinput mzmlsfor mappingNode 101Node 102Node 103R to R MSstatsConverter Table to R R View (Workspace) R to R R to Table R to Table R View (Workspace) R to Table File Importer File Exporter File Importer File Importer URI Port toVariable CSV Reader String to Path(Variable) Connect and set output path in script towrite all plots to a folder Post-processing LFQ results with MSstatsUses MSstatsConverter to make tables that are processed in short R code scripts in various nodes.A consensusXML file from an LFQ workflow is required as input.The outputs are several images and tables accessible through richt clicking the R View and R to Tablenodes. Calculate groupcomparisonsof interestconsensusXMLto MSstats csvstartKNIME workspaceand load data into MSstatsformatQC plotsRename results(spike-ins havefake IDs)all resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-Fwrite allplots to a folderconsensusXMLwrite Filefor backupexperimental designinput mzmlsfor mappingNode 101Node 102Node 103R to R MSstatsConverter Table to R R View (Workspace) R to R R to Table R to Table R View (Workspace) R to Table File Importer File Exporter File Importer File Importer URI Port toVariable CSV Reader String to Path(Variable)

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: alka
Created at: 2018-04-16
On NodePit since: 2019-08-04
Last update: 2025-02-18
Created with KNIME version: v5.4.0
Tags: OpenMSMass SpectrometryMSstatsProtein quantification

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