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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.

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. folder with mzML filesload intermediate fileas tablefolder with fasta databases(e.g., organism + contaminants)startKNIME workspaceand load data into MSstatsformatQC plotsall resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-FNode 24write allplots to a folderinteractive editorGroup comparisons(and rename spike-ins with fake IDs)Node 48Node 49mzTab table format Input Directory File Reader(deprecated) Input Directory Table to R R View (Workspace) R to Table R to Table R View (Workspace) URI Port toVariable R to Table Experimental Design DecoyDatabase PeptideIdentification R To R Output File ProteomicsLFQ MzTabReader 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. folder with mzML filesload intermediate fileas tablefolder with fasta databases(e.g., organism + contaminants)startKNIME workspaceand load data into MSstatsformatQC plotsall resultsspike-in resultsVolcano plot C2 vs C1Spike-ins annotated A-FNode 24write allplots to a folderinteractive editorGroup comparisons(and rename spike-ins with fake IDs)Node 48Node 49mzTab table format Input Directory File Reader(deprecated) Input Directory Table to R R View (Workspace) R to Table R to Table R View (Workspace) URI Port toVariable R to Table Experimental Design DecoyDatabase PeptideIdentification R To R Output File ProteomicsLFQ MzTabReader

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: 2024-04-20
Created with KNIME version: v4.7.1
Tags: OpenMSMass spectrometryProtein identificationProtein quantificationMSstats

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