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

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## 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/

Nodes

• File Exporter3 ×
• File Importer3 ×
• IDFilter2 ×
• Epifany1 ×
• FileMerger1 ×
• Show all 21 nodes

Extensions

• FeatureGeneric Workflow Nodes for KNIME
• FeatureKNIME Base nodes
• FeatureKNIME Basic File System Connectors
• FeatureKNIME Interactive R Statistics Integration
• FeatureKNIME Quick Forms
• Show all 7 modules

Links

• No links available