- Targeted feature detection for label-free quantification
- Parallel execution of OpenMS tools in KNIME
- DNA heteroconjugate detection (Flett et al.)
- Non-targeted LC-MS-based lipidomics
- Basic Peptide Identification
- Consensus Peptide Identification
- Peptide Identification and Label-free Quantification
- Protein Inference
- SWATH Analysis
- Small Molecule Identification and Quantification
This page describes an iTRAQ quantitation and identification workflow.
You have recorded iTRAQ data in HCD/CID mode on an Orbitrap hybrid instrument.
What it does:
Peptide quantitation using the ITRAQAnalyzer tool and FDR-controlled identification using three different search engines, which HCD and CID spectra searched separately (for better FDR).
How to run it:
- Install X!Tandem and OMSSA
- Make sure X!Tandem and OMSSA executables are in your PATH, or point the 4 adapter nodes to the executables
- Enter input mzML files in Node #1, and a FASTA database name in Node #8. You also need the preprocessed .phr version of the FASTA file in the same directory (see OMSSAAdapter docu).
- Enter database and server details for both MascotAdapterOnline nodes
- Check the parameter settings in every node, especially ‘IDMapper’