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Identification_​quantification_​with_​inference_​isobaric_​epifany_​MSstatsTMT

## Description
OpenMS exam workflow for the analysis of isobaric data (e.g. TMT).

A) Quantification via the IsobaricAnalzyer
B) Score estimation and filtering (PSM level)
C) Database search and annotation (target-decoy)
D) Merging of the results
E) Score estimation and protein inference (epifany)
F) Peptide level results
G) Protein level results
H) MSstatsTMT output (peptide level - experimental)

## Input
1) Input files (isobaric labeled peptides (e.g. TMT) as centroided mzML files.
2) Decoy database (.fasta)
3) Experimental Design (.tsv) for MSstatsTMT

## Output
1) MSstatsTMT readble format (.tsv)
2) Peptide level information (.mztab)
3) Protein level information (.csv/mztab)

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" 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/

A) Isobaric experiment (e.g. TMT) C) Database search and annotation(target, decoy) B) Score estimation and filtering(peptide level) D) Merging the results F) Peptide level results G) Protein level results E) Score estimation and proteininference Info: You can build yourown decoy database byusing the OpenMSDecoyDatabase tool. H) Output for MSstatsTMT I) MSstatsTMT analysis via R scripts Identification and quantification for isobaric experimentsUses MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis.Multiple files are written out to the directories specified in the Output Folder nodes in the boxes H, F and G. PEP estimationMerge ID + QuantLoad requiredpackagesInferenceFDR 0.05 (PSM)Actual statistical analysiswith Volcano Plot.Play around with contrasts here.Remove Decoys & ProteinGroup level FDR (0.05)MSstatsTMT_plot_output_directorydecoy database (.fasta)Experimental Designinput (.mzML)Node 262ZipLoopStart PercolatorAdapter ZipLoopEnd ProteinQuantifier IDMapper MzTabExporter IDConflictResolver IsobaricAnalyzer Peptideidentification FileMerger MSstatsConverter URI Port toVariable R Source(Workspace) Epifany IDFilter R View (Workspace) IDFilter StringConfiguration File Importer File Exporter File Importer File Importer File Exporter File Exporter Merge Variables A) Isobaric experiment (e.g. TMT) C) Database search and annotation(target, decoy) B) Score estimation and filtering(peptide level) D) Merging the results F) Peptide level results G) Protein level results E) Score estimation and proteininference Info: You can build yourown decoy database byusing the OpenMSDecoyDatabase tool. H) Output for MSstatsTMT I) MSstatsTMT analysis via R scripts Identification and quantification for isobaric experimentsUses MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis.Multiple files are written out to the directories specified in the Output Folder nodes in the boxes H, F and G. PEP estimationMerge ID + QuantLoad requiredpackagesInferenceFDR 0.05 (PSM)Actual statistical analysiswith Volcano Plot.Play around with contrasts here.Remove Decoys & ProteinGroup level FDR (0.05)MSstatsTMT_plot_output_directorydecoy database (.fasta)Experimental Designinput (.mzML)Node 262ZipLoopStart PercolatorAdapter ZipLoopEnd ProteinQuantifier IDMapper MzTabExporter IDConflictResolver IsobaricAnalyzer Peptideidentification FileMerger MSstatsConverter URI Port toVariable R Source(Workspace) Epifany IDFilter R View (Workspace) IDFilter StringConfiguration File Importer File Exporter File Importer File Importer File Exporter File Exporter Merge Variables

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: 2019-04-29
On NodePit since: 2022-03-01
Last update: 2025-05-01
Created with KNIME version: v5.4.0
Tags: OpenMSMass spectrometryPeptide identificationProtein identificationProtein quantificationMSstats

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